rs2651244

Variant names:

• chr1-70529879-G-A
• rs2651244

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 39 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.126 AC: 5251 AN: 41526

American (AMR) AF: 0.267 AC: 4088 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1560 AN: 3462

East Asian (EAS) AF: 0.142 AC: 736 AN: 5172

South Asian (SAS) AF: 0.304 AC: 1469 AN: 4828

European-Finnish (FIN) AF: 0.427 AC: 4507 AN: 10566

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26324 AN: 67972

Other (OTH) AF: 0.320 AC: 675 AN: 2112

Alfa AF: 0.354 Hom.: 36627

Bravo AF: 0.277

Asia WGS AF: 0.227 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.82
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs2651244; hg19: chr1-70995562;