16-64941298-C-T

Variant names:

• chr16-64941298-C-T
• rs35164

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 0.213 in 152,014 control chromosomes in the GnomAD database, including 3,884 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 (3884 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.277 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: 0.213 AC: 32391 AN: 151896 Hom.: 3880 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.279

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.213 AC: 32409 AN: 152014 Hom.: 3884 Cov.: 32 AF XY: 0.209 AC XY: 15512 AN XY: 74312

African (AFR) AF: 0.103 AC: 4272 AN: 41500

American (AMR) AF: 0.209 AC: 3191 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1032 AN: 3468

East Asian (EAS) AF: 0.205 AC: 1059 AN: 5162

South Asian (SAS) AF: 0.154 AC: 742 AN: 4818

European-Finnish (FIN) AF: 0.210 AC: 2224 AN: 10570

Middle Eastern (MID) AF: 0.279 AC: 81 AN: 290

European-Non Finnish (NFE) AF: 0.281 AC: 19057 AN: 67926

Other (OTH) AF: 0.228 AC: 481 AN: 2110

Alfa AF: 0.237 Hom.: 2624

Bravo AF: 0.210

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.0080
DANN	Benign	0.40
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs35164; hg19: chr16-64975201;