rs6874202

Variant names:

• chr5-156964617-T-C
• rs6874202

Your query was ambiguous. Multiple possible variants found:

• chr5-156964617-T-C
• chr5-156964617-T-G

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 0.572 in 152,050 control chromosomes in the GnomAD database, including 26,200 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 0.57 (26200 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.861
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 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: 0.572 AC: 86925 AN: 151932 Hom.: 26184 Cov.: 33

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.572 AC: 86969 AN: 152050 Hom.: 26200 Cov.: 33 AF XY: 0.580 AC XY: 43100 AN XY: 74342

African (AFR) AF: 0.368 AC: 15273 AN: 41478

American (AMR) AF: 0.686 AC: 10479 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2125 AN: 3468

East Asian (EAS) AF: 0.746 AC: 3860 AN: 5174

South Asian (SAS) AF: 0.677 AC: 3269 AN: 4830

European-Finnish (FIN) AF: 0.684 AC: 7201 AN: 10534

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.627 AC: 42633 AN: 67966

Other (OTH) AF: 0.587 AC: 1239 AN: 2112

Alfa AF: 0.577 Hom.: 3714

Bravo AF: 0.565

Asia WGS AF: 0.688 AC: 2391 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.61
DANN	Benign	0.52
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs6874202; hg19: chr5-156391628; COSMIC: COSV50854535;