rs10220974

Positions:

• chr16-78098377-T-C
• chr16-78098377-T-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 0.772 in 149,736 control chromosomes in the GnomAD database, including 45,513 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 0.77 (45513 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351

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 (EAS) allele frequency at 95% confidence interval = 0.835 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: 0.772 AC: 115518 AN: 149618 Hom.: 45470 Cov.: 28

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.790

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.772 AC: 115612 AN: 149736 Hom.: 45513 Cov.: 28 AF XY: 0.773 AC XY: 56450 AN XY: 73012

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.839

Gnomad4 ASJ AF: 0.850

Gnomad4 EAS AF: 0.856

Gnomad4 SAS AF: 0.821

Gnomad4 FIN AF: 0.808

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.800

Alfa AF: 0.832 Hom.: 85155

Bravo AF: 0.769

Asia WGS AF: 0.803 AC: 2486 AN: 3100

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10220974; hg19: chr16-78132274;