11-102849690-G-A

Variant names:

• chr11-102849690-G-A
• rs613804

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 0.0967 in 152,146 control chromosomes in the GnomAD database, including 976 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 0.097 (976 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0967 AC: 14705 AN: 152028 Hom.: 972 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0691

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0954

Gnomad FIN AF: 0.0407

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0528

Gnomad OTH AF: 0.0975

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

GnomAD4 genome AF: 0.0967 AC: 14711 AN: 152146 Hom.: 976 Cov.: 32 AF XY: 0.0951 AC XY: 7075 AN XY: 74374

African (AFR) AF: 0.188 AC: 7814 AN: 41458

American (AMR) AF: 0.0689 AC: 1052 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 439 AN: 3468

East Asian (EAS) AF: 0.109 AC: 565 AN: 5180

South Asian (SAS) AF: 0.0942 AC: 455 AN: 4828

European-Finnish (FIN) AF: 0.0407 AC: 432 AN: 10606

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0527 AC: 3587 AN: 68010

Other (OTH) AF: 0.102 AC: 215 AN: 2114

Alfa AF: 0.0703 Hom.: 530

Bravo AF: 0.103

Asia WGS AF: 0.109 AC: 379 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.66
DANN	Benign	0.36
PhyloP100		-0.037

Splicing

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

Other links and lift over

dbSNP: rs613804; hg19: chr11-102720421;