10-114431415-A-G

Variant names:

• chr10-114431415-A-G
• rs6646
• NM_002313.7:c.*4845T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002313.7(ABLIM1):​c.*4845T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 152,162 control chromosomes in the GnomAD database, including 48,433 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 0.80 (48430 hom., cov: 32)
  • Exomes 𝑓: 0.75 (3 hom.)
• Consequence: ABLIM1 NM_002313.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• Publications: 8 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABLIM1	NM_002313.7	c.*4845T>C		3_prime_UTR_variant	Exon 23 of 23	ENST00000533213.7	NP_002304.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABLIM1	ENST00000533213.7	c.*4845T>C		3_prime_UTR_variant	Exon 23 of 23	5	NM_002313.7	ENSP00000433629.3
ABLIM1	ENST00000392955.8	c.*4845T>C		3_prime_UTR_variant	Exon 23 of 23	5		ENSP00000376682.4
ABLIM1	ENST00000707119.1	c.*4845T>C		3_prime_UTR_variant	Exon 21 of 21			ENSP00000516747.1
ABLIM1	ENST00000392952.7	c.*4845T>C		3_prime_UTR_variant	Exon 18 of 18	5		ENSP00000376679.3

Frequencies

GnomAD3 genomes AF: 0.796 AC: 121027 AN: 152036 Hom.: 48401 Cov.: 32

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.796

GnomAD4 exome AF: 0.750 AC: 6 AN: 8 Hom.: 3 Cov.: 0 AF XY: 0.750 AC XY: 6 AN XY: 8

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 4 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.796 AC: 121109 AN: 152154 Hom.: 48430 Cov.: 32 AF XY: 0.793 AC XY: 58985 AN XY: 74366

African (AFR) AF: 0.758 AC: 31434 AN: 41474

American (AMR) AF: 0.820 AC: 12540 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.841 AC: 2921 AN: 3472

East Asian (EAS) AF: 0.557 AC: 2883 AN: 5174

South Asian (SAS) AF: 0.819 AC: 3949 AN: 4824

European-Finnish (FIN) AF: 0.778 AC: 8233 AN: 10586

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.830 AC: 56433 AN: 68016

Other (OTH) AF: 0.795 AC: 1679 AN: 2112

Alfa AF: 0.818 Hom.: 188802

Bravo AF: 0.793

Asia WGS AF: 0.717 AC: 2495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.64
PhyloP100		0.16
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6646; hg19: chr10-116191174;