chr11-34437314-T-C

Variant names:

• chr11-34437314-T-C
• rs564250

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 0.778 in 152,118 control chromosomes in the GnomAD database, including 46,122 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 0.78 (46122 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 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: 0.778 AC: 118294 AN: 152000 Hom.: 46102 Cov.: 32

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.778 AC: 118354 AN: 152118 Hom.: 46122 Cov.: 32 AF XY: 0.777 AC XY: 57739 AN XY: 74356

African (AFR) AF: 0.799 AC: 33143 AN: 41472

American (AMR) AF: 0.714 AC: 10924 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2690 AN: 3472

East Asian (EAS) AF: 0.815 AC: 4221 AN: 5180

South Asian (SAS) AF: 0.779 AC: 3761 AN: 4830

European-Finnish (FIN) AF: 0.772 AC: 8154 AN: 10562

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.780 AC: 53053 AN: 67998

Other (OTH) AF: 0.767 AC: 1618 AN: 2110

Alfa AF: 0.773 Hom.: 19452

Bravo AF: 0.774

Asia WGS AF: 0.784 AC: 2724 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.74
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs564250; hg19: chr11-34458861;