rs2651244

Positions:

• chr1-70529879-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 0.296 in 152,128 control chromosomes in the GnomAD database, including 7,724 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 0.30 (7724 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 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: 0.296 AC: 45022 AN: 152010 Hom.: 7722 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.296 AC: 45028 AN: 152128 Hom.: 7724 Cov.: 32 AF XY: 0.295 AC XY: 21949 AN XY: 74354

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.320

Alfa AF: 0.370 Hom.: 15630

Bravo AF: 0.277

Asia WGS AF: 0.227 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2651244; hg19: chr1-70995562;