16-78098377-T-C

Variant names:

• chr16-78098377-T-C
• rs10220974

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.604 AC: 24556 AN: 40688

American (AMR) AF: 0.839 AC: 12606 AN: 15026

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2929 AN: 3444

East Asian (EAS) AF: 0.856 AC: 4282 AN: 5000

South Asian (SAS) AF: 0.821 AC: 3854 AN: 4692

European-Finnish (FIN) AF: 0.808 AC: 8278 AN: 10246

Middle Eastern (MID) AF: 0.795 AC: 232 AN: 292

European-Non Finnish (NFE) AF: 0.838 AC: 56427 AN: 67362

Other (OTH) AF: 0.800 AC: 1671 AN: 2090

Alfa AF: 0.820 Hom.: 192792

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
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs10220974; hg19: chr16-78132274;