11-69767755-A-G

Variant names:

• chr11-69767755-A-G
• rs1944130

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 0.892 in 152,242 control chromosomes in the GnomAD database, including 61,445 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 0.89 (61445 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.955 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: 0.892 AC: 135698 AN: 152124 Hom.: 61411 Cov.: 33

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.947

Gnomad ASJ AF: 0.953

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.961

Gnomad OTH AF: 0.918

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

GnomAD4 genome AF: 0.892 AC: 135789 AN: 152242 Hom.: 61445 Cov.: 33 AF XY: 0.894 AC XY: 66556 AN XY: 74456

African (AFR) AF: 0.718 AC: 29773 AN: 41482

American (AMR) AF: 0.947 AC: 14495 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.953 AC: 3308 AN: 3470

East Asian (EAS) AF: 0.944 AC: 4885 AN: 5176

South Asian (SAS) AF: 0.947 AC: 4572 AN: 4828

European-Finnish (FIN) AF: 0.965 AC: 10247 AN: 10620

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.961 AC: 65385 AN: 68038

Other (OTH) AF: 0.919 AC: 1940 AN: 2112

Alfa AF: 0.919 Hom.: 4357

Bravo AF: 0.883

Asia WGS AF: 0.938 AC: 3262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.25
DANN	Benign	0.24
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs1944130; hg19: chr11-69582523;