16-26254030-C-T

Variant names:

• chr16-26254030-C-T
• rs11644332

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 0.121 in 152,046 control chromosomes in the GnomAD database, including 1,387 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 0.12 (1387 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.173 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: 0.121 AC: 18349 AN: 151928 Hom.: 1386 Cov.: 32

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.0883

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.121 AC: 18357 AN: 152046 Hom.: 1387 Cov.: 32 AF XY: 0.121 AC XY: 9016 AN XY: 74320

African (AFR) AF: 0.0291 AC: 1210 AN: 41524

American (AMR) AF: 0.169 AC: 2572 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 574 AN: 3470

East Asian (EAS) AF: 0.182 AC: 943 AN: 5168

South Asian (SAS) AF: 0.0880 AC: 424 AN: 4818

European-Finnish (FIN) AF: 0.134 AC: 1408 AN: 10544

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10710 AN: 67944

Other (OTH) AF: 0.135 AC: 285 AN: 2114

Alfa AF: 0.0731 Hom.: 89

Bravo AF: 0.123

Asia WGS AF: 0.113 AC: 391 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	3.7
DANN	Benign	0.51
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs11644332; hg19: chr16-26265351;