rs1502172

Positions:

• chr3-135516516-A-G
• chr3-135516516-A-T

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 0.562 in 151,836 control chromosomes in the GnomAD database, including 25,651 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 0.56 (25651 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.665 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: 0.563 AC: 85347 AN: 151718 Hom.: 25634 Cov.: 31

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.562 AC: 85407 AN: 151836 Hom.: 25651 Cov.: 31 AF XY: 0.559 AC XY: 41426 AN XY: 74172

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.614

Alfa AF: 0.647 Hom.: 35409

Bravo AF: 0.564

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.7
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1502172; hg19: chr3-135235358;