rs2749097

Variant names:

• chr1-63661797-C-G
• rs2749097

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 0.19 in 152,104 control chromosomes in the GnomAD database, including 2,949 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 0.19 (2949 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.282 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: 0.190 AC: 28920 AN: 151986 Hom.: 2949 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.190 AC: 28942 AN: 152104 Hom.: 2949 Cov.: 32 AF XY: 0.195 AC XY: 14490 AN XY: 74348

African (AFR) AF: 0.145 AC: 5999 AN: 41502

American (AMR) AF: 0.289 AC: 4417 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 517 AN: 3470

East Asian (EAS) AF: 0.212 AC: 1092 AN: 5152

South Asian (SAS) AF: 0.178 AC: 859 AN: 4814

European-Finnish (FIN) AF: 0.279 AC: 2950 AN: 10562

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12460 AN: 67990

Other (OTH) AF: 0.213 AC: 451 AN: 2116

Alfa AF: 0.184 Hom.: 1523

Bravo AF: 0.190

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.4
DANN	Benign	0.75
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs2749097; hg19: chr1-64127468;