rs11196798

Variant names:

• chr10-114605174-A-C
• rs11196798
• NM_002313.7:c.245-3213T>G

Your query was ambiguous. Multiple possible variants found:

• chr10-114605174-A-C
• chr10-114605174-A-G
• chr10-114605174-A-T

Variant summary

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

The NM_002313.7(ABLIM1):​c.245-3213T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 152,072 control chromosomes in the GnomAD database, including 31,219 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 0.62 (31219 hom., cov: 32)
• Consequence: ABLIM1 NM_002313.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.688
• Publications: 3 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABLIM1	NM_002313.7	c.245-3213T>G		intron_variant	Intron 1 of 22	ENST00000533213.7	NP_002304.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABLIM1	ENST00000533213.7	c.245-3213T>G		intron_variant	Intron 1 of 22	5	NM_002313.7	ENSP00000433629.3

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93657 AN: 151954 Hom.: 31196 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.861

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.616 AC: 93693 AN: 152072 Hom.: 31219 Cov.: 32 AF XY: 0.619 AC XY: 46004 AN XY: 74338

African (AFR) AF: 0.343 AC: 14216 AN: 41478

American (AMR) AF: 0.678 AC: 10351 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2360 AN: 3468

East Asian (EAS) AF: 0.875 AC: 4532 AN: 5180

South Asian (SAS) AF: 0.783 AC: 3768 AN: 4810

European-Finnish (FIN) AF: 0.648 AC: 6834 AN: 10546

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.726 AC: 49347 AN: 68004

Other (OTH) AF: 0.619 AC: 1305 AN: 2108

Alfa AF: 0.667 Hom.: 13076

Bravo AF: 0.606

Asia WGS AF: 0.826 AC: 2872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.20
DANN	Benign	0.53
PhyloP100		-0.69
Mutation Taster		=100/0	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: rs11196798; hg19: chr10-116364933;