rs7731137

chr5-154626094-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 0.622 in 152,042 control chromosomes in the GnomAD database, including 31,048 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 0.62 (31048 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.75 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: 0.622 AC: 94510 AN: 151924 Hom.: 31042 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.622 AC: 94541 AN: 152042 Hom.: 31048 Cov.: 32 AF XY: 0.612 AC XY: 45514 AN XY: 74320

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.757

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.756

Gnomad4 OTH AF: 0.603

Alfa AF: 0.725 Hom.: 25980

Bravo AF: 0.606

Asia WGS AF: 0.514 AC: 1789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.3
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7731137; hg19: chr5-154005654;