chr16-64174077-C-A

Variant names:

• chr16-64174077-C-A
• rs6498937

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 0.211 in 151,962 control chromosomes in the GnomAD database, including 6,323 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 0.21 (6323 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 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: 0.211 AC: 32084 AN: 151844 Hom.: 6313 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.0356

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0672

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.211 AC: 32139 AN: 151962 Hom.: 6323 Cov.: 32 AF XY: 0.210 AC XY: 15602 AN XY: 74296

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.0356

Gnomad4 NFE AF: 0.0672

Gnomad4 OTH AF: 0.173

Alfa AF: 0.0838 Hom.: 1806

Bravo AF: 0.239

Asia WGS AF: 0.231 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.1
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6498937; hg19: chr16-64207981;