16-77684258-T-C

Variant names:

• chr16-77684258-T-C
• rs7198627

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.43 in 152,078 control chromosomes in the GnomAD database, including 14,477 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 0.43 (14477 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.461 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: 0.430 AC: 65334 AN: 151960 Hom.: 14478 Cov.: 33

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.430 AC: 65356 AN: 152078 Hom.: 14477 Cov.: 33 AF XY: 0.429 AC XY: 31919 AN XY: 74348

African (AFR) AF: 0.405 AC: 16786 AN: 41472

American (AMR) AF: 0.368 AC: 5614 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1488 AN: 3470

East Asian (EAS) AF: 0.194 AC: 1004 AN: 5178

South Asian (SAS) AF: 0.457 AC: 2202 AN: 4814

European-Finnish (FIN) AF: 0.489 AC: 5167 AN: 10562

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31630 AN: 67992

Other (OTH) AF: 0.415 AC: 876 AN: 2110

Alfa AF: 0.441 Hom.: 46359

Bravo AF: 0.414

Asia WGS AF: 0.318 AC: 1109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	14
DANN	Benign	0.75
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs7198627; hg19: chr16-77718155;