rs4620978

Variant names:

• chr16-62158800-A-C
• rs4620978

Your query was ambiguous. Multiple possible variants found:

• chr16-62158800-A-C
• chr16-62158800-A-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 0.476 in 151,958 control chromosomes in the GnomAD database, including 17,792 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 0.48 (17792 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 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: 0.476 AC: 72318 AN: 151838 Hom.: 17775 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.476 AC: 72387 AN: 151958 Hom.: 17792 Cov.: 32 AF XY: 0.484 AC XY: 35908 AN XY: 74246

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.502

Alfa AF: 0.490 Hom.: 24304

Bravo AF: 0.470

Asia WGS AF: 0.690 AC: 2397 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.61
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4620978; hg19: chr16-62192704;