rs11944965

Variant names:

• chr4-62558371-C-T
• rs11944965

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 0.339 in 152,004 control chromosomes in the GnomAD database, including 9,135 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 0.34 (9135 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.744
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 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: 0.339 AC: 51448 AN: 151884 Hom.: 9131 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.339 AC: 51488 AN: 152004 Hom.: 9135 Cov.: 32 AF XY: 0.338 AC XY: 25149 AN XY: 74304

African (AFR) AF: 0.315 AC: 13081 AN: 41462

American (AMR) AF: 0.352 AC: 5379 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1211 AN: 3470

East Asian (EAS) AF: 0.684 AC: 3517 AN: 5144

South Asian (SAS) AF: 0.391 AC: 1888 AN: 4828

European-Finnish (FIN) AF: 0.257 AC: 2721 AN: 10570

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22524 AN: 67950

Other (OTH) AF: 0.357 AC: 754 AN: 2112

Alfa AF: 0.344 Hom.: 36515

Bravo AF: 0.346

Asia WGS AF: 0.490 AC: 1703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.72
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs11944965; hg19: chr4-63424089;