rs11802770

Variant names:

• chr1-38255991-T-C
• rs11802770

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 0.555 in 152,010 control chromosomes in the GnomAD database, including 23,719 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 0.55 (23719 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.851
• 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 (EAS) allele frequency at 95% confidence interval = 0.665 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: 0.555 AC: 84225 AN: 151892 Hom.: 23702 Cov.: 32

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.555 AC: 84298 AN: 152010 Hom.: 23719 Cov.: 32 AF XY: 0.555 AC XY: 41253 AN XY: 74312

African (AFR) AF: 0.646 AC: 26785 AN: 41472

American (AMR) AF: 0.531 AC: 8109 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1455 AN: 3468

East Asian (EAS) AF: 0.684 AC: 3527 AN: 5154

South Asian (SAS) AF: 0.570 AC: 2746 AN: 4814

European-Finnish (FIN) AF: 0.485 AC: 5128 AN: 10564

Middle Eastern (MID) AF: 0.476 AC: 138 AN: 290

European-Non Finnish (NFE) AF: 0.511 AC: 34750 AN: 67956

Other (OTH) AF: 0.546 AC: 1155 AN: 2114

Alfa AF: 0.526 Hom.: 83846

Bravo AF: 0.556

Asia WGS AF: 0.637 AC: 2218 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	0.0070
DANN	Benign	0.39
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs11802770; hg19: chr1-38721663;