rs2749097

Variant names:

• chr1-63661797-C-G
• rs2749097

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 0.19 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.213

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2749097; hg19: chr1-64127468;