rs2470644

Positions:

• chr3-5735170-T-C
• chr3-5735170-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 0.225 in 152,164 control chromosomes in the GnomAD database, including 8,454 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 0.23 (8454 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34148 AN: 152044 Hom.: 8410 Cov.: 32

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0926

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.0376

Gnomad FIN AF: 0.0533

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0587

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.225 AC: 34257 AN: 152164 Hom.: 8454 Cov.: 32 AF XY: 0.219 AC XY: 16313 AN XY: 74418

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.0926

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.0373

Gnomad4 FIN AF: 0.0533

Gnomad4 NFE AF: 0.0587

Gnomad4 OTH AF: 0.200

Alfa AF: 0.0873 Hom.: 1659

Bravo AF: 0.254

Asia WGS AF: 0.158 AC: 550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.68
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2470644; hg19: chr3-5776857;