rs26868

Variant names:

• chr16-2199375-T-A
• rs26868

Your query was ambiguous. Multiple possible variants found:

• chr16-2199375-T-A
• chr16-2199375-T-C

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 0.348 in 151,934 control chromosomes in the GnomAD database, including 11,318 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 0.35 (11318 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310
• Publications: 39 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 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: 0.348 AC: 52852 AN: 151816 Hom.: 11320 Cov.: 32

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.348 AC: 52861 AN: 151934 Hom.: 11318 Cov.: 32 AF XY: 0.351 AC XY: 26072 AN XY: 74236

African (AFR) AF: 0.0946 AC: 3920 AN: 41448

American (AMR) AF: 0.433 AC: 6614 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1211 AN: 3468

East Asian (EAS) AF: 0.526 AC: 2707 AN: 5144

South Asian (SAS) AF: 0.491 AC: 2369 AN: 4820

European-Finnish (FIN) AF: 0.423 AC: 4471 AN: 10572

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.448 AC: 30434 AN: 67914

Other (OTH) AF: 0.354 AC: 744 AN: 2104

Alfa AF: 0.399 Hom.: 1752

Bravo AF: 0.335

Asia WGS AF: 0.475 AC: 1648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.1
DANN	Benign	0.50
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs26868; hg19: chr16-2249376;