rs1481963

Variant names:

• chr11-103523199-G-A
• rs1481963
• ENST00000827359.1:n.219-3972C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-103523199-G-A
• chr11-103523199-G-T

Variant summary

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

The ENST00000827359.1(ENSG00000307600):​n.219-3972C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,220 control chromosomes in the GnomAD database, including 29,433 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 0.60 (29433 hom., cov: 32)
• Consequence: ENSG00000307600 ENST00000827359.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.873
• Publications: 4 publications found

Genes affected

ENSG00000307600 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307600	ENST00000827359.1	n.219-3972C>T		intron_variant	Intron 2 of 2
ENSG00000307600	ENST00000827360.1	n.93-3972C>T		intron_variant	Intron 1 of 1
ENSG00000307600	ENST00000827361.1	n.106-3972C>T		intron_variant	Intron 1 of 1
ENSG00000307600	ENST00000827362.1	n.227+3762C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91105 AN: 151104 Hom.: 29431 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.603 AC: 91129 AN: 151220 Hom.: 29433 Cov.: 32 AF XY: 0.606 AC XY: 44777 AN XY: 73924

African (AFR) AF: 0.338 AC: 13809 AN: 40884

American (AMR) AF: 0.699 AC: 10646 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2458 AN: 3460

East Asian (EAS) AF: 0.736 AC: 3802 AN: 5166

South Asian (SAS) AF: 0.665 AC: 3183 AN: 4788

European-Finnish (FIN) AF: 0.689 AC: 7239 AN: 10512

Middle Eastern (MID) AF: 0.707 AC: 205 AN: 290

European-Non Finnish (NFE) AF: 0.705 AC: 47842 AN: 67874

Other (OTH) AF: 0.638 AC: 1344 AN: 2106

Alfa AF: 0.632 Hom.: 5400

Bravo AF: 0.592

Asia WGS AF: 0.663 AC: 2303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.91
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs1481963; hg19: chr11-103393927;