rs985273

Variant names:

• chr10-114575487-G-A
• rs985273
• NM_002313.7:c.492C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-114575487-G-A
• chr10-114575487-G-C
• chr10-114575487-G-T

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The NM_002313.7(ABLIM1):​c.492C>T​(p.Phe164Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 1,613,882 control chromosomes in the GnomAD database, including 36,147 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.26 (6375 hom., cov: 32)
  • Exomes 𝑓: 0.19 (29772 hom.)
• Consequence: ABLIM1 NM_002313.7 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 14 publications found

Genes affected

ABLIM1 (HGNC:78): (actin binding LIM protein 1) This gene encodes a LIM zinc-binding domain-containing protein that binds to actin filaments and mediates interactions between actin and cytoplasmic targets. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jun 2017]

ACMG classification

Our verdict: Benign. The variant received -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BP7: Synonymous conserved (PhyloP=0.308 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002313.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABLIM1	NM_002313.7	MANE Select	c.492C>T	p.Phe164Phe	synonymous	Exon 3 of 23	NP_002304.3
	ABLIM1	NM_001322882.2		c.312C>T	p.Phe104Phe	synonymous	Exon 3 of 24	NP_001309811.1	O14639-6
	ABLIM1	NM_001003407.2		c.312C>T	p.Phe104Phe	synonymous	Exon 3 of 23	NP_001003407.1	O14639-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABLIM1	ENST00000533213.7	TSL:5 MANE Select	c.492C>T	p.Phe164Phe	synonymous	Exon 3 of 23	ENSP00000433629.3	O14639-1
	ABLIM1	ENST00000649363.1		c.492C>T	p.Phe164Phe	synonymous	Exon 3 of 25	ENSP00000497150.1	A0A3B3IS55
	ABLIM1	ENST00000369256.6	TSL:5	c.312C>T	p.Phe104Phe	synonymous	Exon 3 of 24	ENSP00000358260.3	O14639-6

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40069 AN: 151924 Hom.: 6361 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.280

GnomAD2 exomes AF: 0.218 AC: 54733 AN: 251250 AF XY: 0.208

Gnomad AFR exome AF: 0.438

Gnomad AMR exome AF: 0.314

Gnomad ASJ exome AF: 0.233

Gnomad EAS exome AF: 0.231

Gnomad FIN exome AF: 0.115

Gnomad NFE exome AF: 0.181

Gnomad OTH exome AF: 0.228

GnomAD4 exome AF: 0.194 AC: 283517 AN: 1461840 Hom.: 29772 Cov.: 33 AF XY: 0.193 AC XY: 140029 AN XY: 727228

African (AFR) AF: 0.448 AC: 15007 AN: 33480

American (AMR) AF: 0.317 AC: 14171 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 6018 AN: 26136

East Asian (EAS) AF: 0.238 AC: 9444 AN: 39700

South Asian (SAS) AF: 0.184 AC: 15887 AN: 86258

European-Finnish (FIN) AF: 0.118 AC: 6311 AN: 53418

Middle Eastern (MID) AF: 0.271 AC: 1566 AN: 5768

European-Non Finnish (NFE) AF: 0.182 AC: 202148 AN: 1111960

Other (OTH) AF: 0.215 AC: 12965 AN: 60396

GnomAD4 genome AF: 0.264 AC: 40136 AN: 152042 Hom.: 6375 Cov.: 32 AF XY: 0.261 AC XY: 19426 AN XY: 74322

African (AFR) AF: 0.434 AC: 17997 AN: 41422

American (AMR) AF: 0.322 AC: 4922 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 838 AN: 3472

East Asian (EAS) AF: 0.223 AC: 1155 AN: 5176

South Asian (SAS) AF: 0.196 AC: 943 AN: 4816

European-Finnish (FIN) AF: 0.120 AC: 1266 AN: 10586

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.178 AC: 12071 AN: 67982

Other (OTH) AF: 0.276 AC: 581 AN: 2104

Alfa AF: 0.216 Hom.: 12601

Bravo AF: 0.288

Asia WGS AF: 0.224 AC: 777 AN: 3478

EpiCase AF: 0.198

EpiControl AF: 0.193

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	8.8
DANN	Benign	0.78
PhyloP100		0.31
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs985273; hg19: chr10-116335246; COSMIC: COSV53302556;