rs270654

Variant names:

• chr5-159138101-T-C
• rs270654

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 0.0715 in 152,292 control chromosomes in the GnomAD database, including 511 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 0.072 (511 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 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: 0.0716 AC: 10896 AN: 152174 Hom.: 511 Cov.: 32

Gnomad AFR AF: 0.0188

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0642

Gnomad ASJ AF: 0.0763

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0623

Gnomad FIN AF: 0.0961

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0828

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

GnomAD4 genome AF: 0.0715 AC: 10889 AN: 152292 Hom.: 511 Cov.: 32 AF XY: 0.0697 AC XY: 5188 AN XY: 74470

Gnomad4 AFR AF: 0.0188

Gnomad4 AMR AF: 0.0641

Gnomad4 ASJ AF: 0.0763

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0617

Gnomad4 FIN AF: 0.0961

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0810

Alfa AF: 0.0986 Hom.: 1086

Bravo AF: 0.0657

Asia WGS AF: 0.0190 AC: 66 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs270654; hg19: chr5-158565109; COSMIC: COSV60222470;