rs2896159

Variant names:

• chr7-115562480-T-C
• rs2896159

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 0.335 in 151,792 control chromosomes in the GnomAD database, including 8,676 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 0.34 (8676 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.899

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.431 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: 0.335 AC: 50817 AN: 151674 Hom.: 8661 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.335 AC: 50873 AN: 151792 Hom.: 8676 Cov.: 32 AF XY: 0.336 AC XY: 24964 AN XY: 74204

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.338

Alfa AF: 0.326 Hom.: 16592

Bravo AF: 0.349

Asia WGS AF: 0.393 AC: 1367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.9
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2896159; hg19: chr7-115202534;