16-64940451-C-T

Variant names:

• chr16-64940451-C-T
• rs35168

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 0.91 in 152,148 control chromosomes in the GnomAD database, including 63,014 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 0.91 (63014 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.821

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.910 AC: 138299 AN: 152030 Hom.: 62961 Cov.: 31

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.892

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.903

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.910 AC: 138412 AN: 152148 Hom.: 63014 Cov.: 31 AF XY: 0.911 AC XY: 67725 AN XY: 74370

Gnomad4 AFR AF: 0.912

Gnomad4 AMR AF: 0.892

Gnomad4 ASJ AF: 0.927

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.948

Gnomad4 FIN AF: 0.896

Gnomad4 NFE AF: 0.903

Gnomad4 OTH AF: 0.920

Alfa AF: 0.908 Hom.: 7783

Bravo AF: 0.911

Asia WGS AF: 0.962 AC: 3344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.7
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35168; hg19: chr16-64974354;