rs11203405

Variant names:

• chr1-17481041-A-G
• rs11203405

Your query was ambiguous. Multiple possible variants found:

• chr1-17481041-A-G
• chr1-17481041-A-T

Variant summary

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

The variant allele was found at a frequency of 0.588 in 151,942 control chromosomes in the GnomAD database, including 26,932 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 0.59 (26932 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.697 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

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89341 AN: 151822 Hom.: 26919 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.790

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.588 AC: 89389 AN: 151942 Hom.: 26932 Cov.: 32 AF XY: 0.582 AC XY: 43189 AN XY: 74264

African (AFR) AF: 0.476 AC: 19717 AN: 41438

American (AMR) AF: 0.708 AC: 10779 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2528 AN: 3468

East Asian (EAS) AF: 0.642 AC: 3304 AN: 5150

South Asian (SAS) AF: 0.572 AC: 2753 AN: 4816

European-Finnish (FIN) AF: 0.499 AC: 5275 AN: 10564

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.631 AC: 42886 AN: 67966

Other (OTH) AF: 0.591 AC: 1245 AN: 2108

Alfa AF: 0.627 Hom.: 31177

Bravo AF: 0.600

Asia WGS AF: 0.607 AC: 2111 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	2.0
DANN	Benign	0.69
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs11203405; hg19: chr1-17807537; COSMIC: COSV59927676;