rs26865

Variant names:

• chr16-2203772-A-G
• rs26865

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 0.416 in 152,074 control chromosomes in the GnomAD database, including 15,899 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 0.42 (15899 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

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 = 0.568 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: 0.416 AC: 63265 AN: 151956 Hom.: 15902 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.416 AC: 63278 AN: 152074 Hom.: 15899 Cov.: 32 AF XY: 0.422 AC XY: 31382 AN XY: 74342

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.417

Alfa AF: 0.496 Hom.: 19229

Bravo AF: 0.394

Asia WGS AF: 0.521 AC: 1807 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	2.3
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs26865; hg19: chr16-2253773;