16-64940451-C-T

Variant names:

• chr16-64940451-C-T
• rs35168

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 0.91 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.912 AC: 37860 AN: 41510

American (AMR) AF: 0.892 AC: 13616 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.927 AC: 3217 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5172 AN: 5176

South Asian (SAS) AF: 0.948 AC: 4567 AN: 4816

European-Finnish (FIN) AF: 0.896 AC: 9497 AN: 10598

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.903 AC: 61432 AN: 67998

Other (OTH) AF: 0.920 AC: 1941 AN: 2110

Alfa AF: 0.908 Hom.: 8116

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
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs35168; hg19: chr16-64974354;