rs1001254

Variant names:

• chr3-7892646-C-G
• rs1001254

Your query was ambiguous. Multiple possible variants found:

• chr3-7892646-C-G
• chr3-7892646-C-T

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 0.114 in 152,060 control chromosomes in the GnomAD database, including 1,119 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 0.11 (1119 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.141 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: 0.114 AC: 17362 AN: 151942 Hom.: 1116 Cov.: 31

Gnomad AFR AF: 0.0868

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.0894

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.00347

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.114 AC: 17370 AN: 152060 Hom.: 1119 Cov.: 31 AF XY: 0.112 AC XY: 8346 AN XY: 74328

African (AFR) AF: 0.0867 AC: 3599 AN: 41490

American (AMR) AF: 0.0894 AC: 1365 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 448 AN: 3472

East Asian (EAS) AF: 0.00329 AC: 17 AN: 5172

South Asian (SAS) AF: 0.105 AC: 507 AN: 4818

European-Finnish (FIN) AF: 0.126 AC: 1333 AN: 10572

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9725 AN: 67958

Other (OTH) AF: 0.106 AC: 223 AN: 2112

Alfa AF: 0.0817 Hom.: 117

Bravo AF: 0.108

Asia WGS AF: 0.0690 AC: 241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
DANN	Benign	0.81
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1001254; hg19: chr3-7934333;