rs11586310

Variant names:

• chr1-234700462-T-C
• rs11586310

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 0.0472 in 152,300 control chromosomes in the GnomAD database, including 200 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 0.047 (200 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0642 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: 0.0471 AC: 7166 AN: 152182 Hom.: 199 Cov.: 32

Gnomad AFR AF: 0.0430

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0675

Gnomad ASJ AF: 0.0210

Gnomad EAS AF: 0.0568

Gnomad SAS AF: 0.0255

Gnomad FIN AF: 0.0571

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0459

Gnomad OTH AF: 0.0358

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

GnomAD4 genome AF: 0.0472 AC: 7185 AN: 152300 Hom.: 200 Cov.: 32 AF XY: 0.0477 AC XY: 3549 AN XY: 74458

African (AFR) AF: 0.0433 AC: 1800 AN: 41566

American (AMR) AF: 0.0676 AC: 1035 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0210 AC: 73 AN: 3472

East Asian (EAS) AF: 0.0569 AC: 295 AN: 5182

South Asian (SAS) AF: 0.0253 AC: 122 AN: 4828

European-Finnish (FIN) AF: 0.0571 AC: 605 AN: 10600

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0459 AC: 3122 AN: 68026

Other (OTH) AF: 0.0354 AC: 75 AN: 2116

Alfa AF: 0.0518 Hom.: 37

Bravo AF: 0.0490

Asia WGS AF: 0.0420 AC: 145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.0
DANN	Benign	0.78
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs11586310; hg19: chr1-234836209;