rs61810702

chr1-115127988-G-A

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 0.28 in 152,186 control chromosomes in the GnomAD database, including 6,384 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 0.28 (6384 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 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: 0.280 AC: 42584 AN: 152070 Hom.: 6383 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.280 AC: 42605 AN: 152186 Hom.: 6384 Cov.: 33 AF XY: 0.287 AC XY: 21362 AN XY: 74396

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.288

Alfa AF: 0.269 Hom.: 1084

Bravo AF: 0.283

Asia WGS AF: 0.403 AC: 1401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	2.0
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs61810702; hg19: chr1-115670609; COSMIC: COSV59990423;