16-174620-T-C

Variant names:

• chr16-174620-T-C
• rs2238369

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 0.404 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.398

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2238369; hg19: chr16-224619;