16-26249467-T-C

Variant names:

• chr16-26249467-T-C
• rs3096425

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 0.879 in 152,020 control chromosomes in the GnomAD database, including 59,175 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 0.88 (59175 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.599
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.915 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: 0.879 AC: 133549 AN: 151902 Hom.: 59123 Cov.: 31

Gnomad AFR AF: 0.922

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.879 AC: 133655 AN: 152020 Hom.: 59175 Cov.: 31 AF XY: 0.870 AC XY: 64623 AN XY: 74282

African (AFR) AF: 0.922 AC: 38272 AN: 41498

American (AMR) AF: 0.761 AC: 11608 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.918 AC: 3185 AN: 3470

East Asian (EAS) AF: 0.700 AC: 3587 AN: 5124

South Asian (SAS) AF: 0.800 AC: 3857 AN: 4822

European-Finnish (FIN) AF: 0.815 AC: 8620 AN: 10576

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.907 AC: 61610 AN: 67964

Other (OTH) AF: 0.881 AC: 1857 AN: 2108

Alfa AF: 0.892 Hom.: 47952

Bravo AF: 0.877

Asia WGS AF: 0.768 AC: 2670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.9
DANN	Benign	0.63
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs3096425; hg19: chr16-26260788;