4-77684215-A-G

Variant names:

• chr4-77684215-A-G
• rs958617

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 0.567 in 152,032 control chromosomes in the GnomAD database, including 28,561 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 0.57 (28561 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.722

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.724 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: 0.567 AC: 86209 AN: 151914 Hom.: 28564 Cov.: 31

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.567 AC: 86212 AN: 152032 Hom.: 28561 Cov.: 31 AF XY: 0.568 AC XY: 42183 AN XY: 74302

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.588

Alfa AF: 0.692 Hom.: 36156

Bravo AF: 0.540

Asia WGS AF: 0.575 AC: 1998 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	3.4
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs958617; hg19: chr4-78605369;