4-44962936-C-G

Position:

• chr4-44962936-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.905 in 152,056 control chromosomes in the GnomAD database, including 62,724 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 0.91 (62724 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.905 AC: 137532 AN: 151938 Hom.: 62680 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.944

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.914

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.910

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

GnomAD4 genome AF: 0.905 AC: 137633 AN: 152056 Hom.: 62724 Cov.: 32 AF XY: 0.910 AC XY: 67636 AN XY: 74338

Gnomad4 AFR AF: 0.777

Gnomad4 AMR AF: 0.945

Gnomad4 ASJ AF: 0.954

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.981

Gnomad4 FIN AF: 0.969

Gnomad4 NFE AF: 0.949

Gnomad4 OTH AF: 0.911

Alfa AF: 0.926 Hom.: 8139

Bravo AF: 0.896

Asia WGS AF: 0.978 AC: 3395 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	8.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1908806; hg19: chr4-44964953;