rs2896159

Variant names:

• chr7-115562480-T-C
• rs2896159

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 0.335 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• 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

African (AFR) AF: 0.321 AC: 13306 AN: 41424

American (AMR) AF: 0.440 AC: 6703 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1155 AN: 3466

East Asian (EAS) AF: 0.387 AC: 1989 AN: 5140

South Asian (SAS) AF: 0.291 AC: 1402 AN: 4820

European-Finnish (FIN) AF: 0.296 AC: 3128 AN: 10564

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 21956 AN: 67840

Other (OTH) AF: 0.338 AC: 711 AN: 2104

Alfa AF: 0.327 Hom.: 34547

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
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs2896159; hg19: chr7-115202534;