11-69258332-T-G

Variant names:

• chr11-69258332-T-G
• rs3884627

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 0.761 in 152,076 control chromosomes in the GnomAD database, including 45,202 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 0.76 (45202 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 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: 0.761 AC: 115669 AN: 151958 Hom.: 45136 Cov.: 31

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.761 AC: 115794 AN: 152076 Hom.: 45202 Cov.: 31 AF XY: 0.763 AC XY: 56690 AN XY: 74334

African (AFR) AF: 0.937 AC: 38911 AN: 41518

American (AMR) AF: 0.756 AC: 11548 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 2503 AN: 3472

East Asian (EAS) AF: 0.604 AC: 3118 AN: 5166

South Asian (SAS) AF: 0.591 AC: 2848 AN: 4816

European-Finnish (FIN) AF: 0.750 AC: 7923 AN: 10566

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.686 AC: 46643 AN: 67944

Other (OTH) AF: 0.746 AC: 1576 AN: 2112

Alfa AF: 0.710 Hom.: 60302

Bravo AF: 0.773

Asia WGS AF: 0.674 AC: 2341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.85
DANN	Benign	0.39
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs3884627; hg19: chr11-69025799;