rs941853

Variant names:

• chr10-114439416-G-A
• rs941853
• NM_002313.7:c.2068-166C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002313.7(ABLIM1):​c.2068-166C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,138 control chromosomes in the GnomAD database, including 3,385 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 0.20 (3385 hom., cov: 33)
• Consequence: ABLIM1 NM_002313.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABLIM1	NM_002313.7	c.2068-166C>T		intron_variant	Intron 20 of 22	ENST00000533213.7	NP_002304.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABLIM1	ENST00000533213.7	c.2068-166C>T		intron_variant	Intron 20 of 22	5	NM_002313.7	ENSP00000433629.3

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29930 AN: 152020 Hom.: 3383 Cov.: 33

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.185

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.197 AC: 29973 AN: 152138 Hom.: 3385 Cov.: 33 AF XY: 0.196 AC XY: 14600 AN XY: 74384

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.182

Alfa AF: 0.155 Hom.: 2576

Bravo AF: 0.204

Asia WGS AF: 0.189 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs941853; hg19: chr10-116199175;