16-174620-T-C

Variant names:

• chr16-174620-T-C
• rs2238369

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 0.404 in 148,416 control chromosomes in the GnomAD database, including 14,045 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 0.40 (14045 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.822
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.46 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: 0.404 AC: 59892 AN: 148298 Hom.: 14034 Cov.: 31

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.407

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.404 AC: 59923 AN: 148416 Hom.: 14045 Cov.: 31 AF XY: 0.405 AC XY: 29344 AN XY: 72510

African (AFR) AF: 0.268 AC: 10254 AN: 38332

American (AMR) AF: 0.420 AC: 6338 AN: 15084

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1695 AN: 3460

East Asian (EAS) AF: 0.325 AC: 1673 AN: 5140

South Asian (SAS) AF: 0.382 AC: 1764 AN: 4612

European-Finnish (FIN) AF: 0.493 AC: 5208 AN: 10564

Middle Eastern (MID) AF: 0.414 AC: 120 AN: 290

European-Non Finnish (NFE) AF: 0.465 AC: 31560 AN: 67920

Other (OTH) AF: 0.398 AC: 836 AN: 2102

Alfa AF: 0.305 Hom.: 893

Bravo AF: 0.391

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.55
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs2238369; hg19: chr16-224619;