chr11-69517617-G-T

Variant names:

• chr11-69517617-G-T
• rs634300

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 0.523 in 151,940 control chromosomes in the GnomAD database, including 24,318 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 0.52 (24318 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 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: 0.522 AC: 79274 AN: 151822 Hom.: 24262 Cov.: 32

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.523 AC: 79394 AN: 151940 Hom.: 24318 Cov.: 32 AF XY: 0.530 AC XY: 39360 AN XY: 74244

African (AFR) AF: 0.835 AC: 34647 AN: 41470

American (AMR) AF: 0.522 AC: 7969 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1169 AN: 3470

East Asian (EAS) AF: 0.791 AC: 4087 AN: 5166

South Asian (SAS) AF: 0.441 AC: 2122 AN: 4816

European-Finnish (FIN) AF: 0.451 AC: 4744 AN: 10524

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.342 AC: 23251 AN: 67900

Other (OTH) AF: 0.471 AC: 996 AN: 2114

Alfa AF: 0.290 Hom.: 978

Bravo AF: 0.542

Asia WGS AF: 0.620 AC: 2152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.75
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs634300; hg19: chr11-69332385;