4-15939760-G-C

Variant names:

• chr4-15939760-G-C
• rs2246196

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 0.955 in 152,296 control chromosomes in the GnomAD database, including 69,546 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 0.96 (69546 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.958 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: 0.955 AC: 145352 AN: 152178 Hom.: 69491 Cov.: 33

Gnomad AFR AF: 0.941

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.963

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.972

Gnomad FIN AF: 0.987

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.964

Gnomad OTH AF: 0.957

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

GnomAD4 genome AF: 0.955 AC: 145464 AN: 152296 Hom.: 69546 Cov.: 33 AF XY: 0.956 AC XY: 71181 AN XY: 74462

Gnomad4 AFR AF: 0.941

Gnomad4 AMR AF: 0.963

Gnomad4 ASJ AF: 0.978

Gnomad4 EAS AF: 0.818

Gnomad4 SAS AF: 0.973

Gnomad4 FIN AF: 0.987

Gnomad4 NFE AF: 0.964

Gnomad4 OTH AF: 0.954

Alfa AF: 0.964 Hom.: 8332

Bravo AF: 0.952

Asia WGS AF: 0.883 AC: 3073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2246196; hg19: chr4-15941383;