rs2897047

Variant names:

• chr5-2640009-A-G
• rs2897047

Your query was ambiguous. Multiple possible variants found:

• chr5-2640009-A-G
• chr5-2640009-A-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 0.626 in 151,800 control chromosomes in the GnomAD database, including 30,217 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 0.63 (30217 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.689
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.676 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: 0.626 AC: 94991 AN: 151680 Hom.: 30204 Cov.: 30

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.673

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.626 AC: 95046 AN: 151800 Hom.: 30217 Cov.: 30 AF XY: 0.626 AC XY: 46451 AN XY: 74160

African (AFR) AF: 0.539 AC: 22291 AN: 41364

American (AMR) AF: 0.591 AC: 9011 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2422 AN: 3464

East Asian (EAS) AF: 0.488 AC: 2498 AN: 5122

South Asian (SAS) AF: 0.659 AC: 3154 AN: 4784

European-Finnish (FIN) AF: 0.688 AC: 7269 AN: 10560

Middle Eastern (MID) AF: 0.666 AC: 193 AN: 290

European-Non Finnish (NFE) AF: 0.681 AC: 46279 AN: 67950

Other (OTH) AF: 0.629 AC: 1325 AN: 2108

Alfa AF: 0.650 Hom.: 11810

Bravo AF: 0.614

Asia WGS AF: 0.607 AC: 2114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.38
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs2897047; hg19: chr5-2640123;