5-35231371-T-G

Position:

• chr5-35231371-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 0.0602 in 150,512 control chromosomes in the GnomAD database, including 343 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 0.060 (343 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.126 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: 0.0603 AC: 9066 AN: 150398 Hom.: 343 Cov.: 31

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0778

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0391

Gnomad FIN AF: 0.0748

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0674

Gnomad OTH AF: 0.0652

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

GnomAD4 genome AF: 0.0602 AC: 9065 AN: 150512 Hom.: 343 Cov.: 31 AF XY: 0.0610 AC XY: 4485 AN XY: 73550

Gnomad4 AFR AF: 0.0274

Gnomad4 AMR AF: 0.0778

Gnomad4 ASJ AF: 0.0945

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.0401

Gnomad4 FIN AF: 0.0748

Gnomad4 NFE AF: 0.0674

Gnomad4 OTH AF: 0.0645

Alfa AF: 0.0212 Hom.: 26

Bravo AF: 0.0601

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.24
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7701473; hg19: chr5-35231473;