rs6670495

chr1-46722236-T-Achr1-46722236-T-Cchr1-46722236-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 0.409 in 151,872 control chromosomes in the GnomAD database, including 15,229 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 0.41 (15229 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.78 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: 0.409 AC: 62021 AN: 151754 Hom.: 15174 Cov.: 31

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.409 AC: 62143 AN: 151872 Hom.: 15229 Cov.: 31 AF XY: 0.416 AC XY: 30847 AN XY: 74194

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.800

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.418

Alfa AF: 0.322 Hom.: 1152

Bravo AF: 0.428

Asia WGS AF: 0.624 AC: 2171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.85
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6670495; hg19: chr1-47187908;