rs6874202

chr5-156964617-T-Cchr5-156964617-T-G

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 0.572 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.587

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

Splicing

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

Publications

LitVar

Other links and lift over

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