rs1426897

Variant names:

• chr15-26520713-G-A
• rs1426897

Your query was ambiguous. Multiple possible variants found:

• chr15-26520713-G-A
• chr15-26520713-G-C
• chr15-26520713-G-T

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 0.352 in 151,884 control chromosomes in the GnomAD database, including 10,076 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 (10076 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 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: 0.352 AC: 53459 AN: 151766 Hom.: 10084 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.352 AC: 53455 AN: 151884 Hom.: 10076 Cov.: 32 AF XY: 0.354 AC XY: 26258 AN XY: 74224

African (AFR) AF: 0.212 AC: 8756 AN: 41390

American (AMR) AF: 0.361 AC: 5505 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1221 AN: 3468

East Asian (EAS) AF: 0.183 AC: 947 AN: 5166

South Asian (SAS) AF: 0.382 AC: 1839 AN: 4818

European-Finnish (FIN) AF: 0.433 AC: 4554 AN: 10520

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29358 AN: 67946

Other (OTH) AF: 0.390 AC: 822 AN: 2108

Alfa AF: 0.237 Hom.: 548

Bravo AF: 0.340

Asia WGS AF: 0.297 AC: 1035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.18
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs1426897; hg19: chr15-26765860;