rs2974097

chr5-86038135-T-Achr5-86038135-T-Cchr5-86038135-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 0.504 in 151,966 control chromosomes in the GnomAD database, including 20,495 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 0.50 (20495 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 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: 0.504 AC: 76522 AN: 151848 Hom.: 20466 Cov.: 32

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.504 AC: 76594 AN: 151966 Hom.: 20495 Cov.: 32 AF XY: 0.504 AC XY: 37428 AN XY: 74268

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.494

Alfa AF: 0.312 Hom.: 704

Bravo AF: 0.520

Asia WGS AF: 0.291 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.5
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2974097; hg19: chr5-85333953;