chr5-35231371-T-G

Variant names:

• chr5-35231371-T-G
• rs7701473

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;