rs12041748

Variant names:

• chr1-239061247-A-C
• rs12041748

Your query was ambiguous. Multiple possible variants found:

• chr1-239061247-A-C
• chr1-239061247-A-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 0.125 in 151,960 control chromosomes in the GnomAD database, including 1,270 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 0.12 (1270 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.21 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: 0.125 AC: 18968 AN: 151846 Hom.: 1267 Cov.: 32

Gnomad AFR AF: 0.0914

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.125 AC: 18987 AN: 151960 Hom.: 1270 Cov.: 32 AF XY: 0.127 AC XY: 9426 AN XY: 74292

African (AFR) AF: 0.0913 AC: 3788 AN: 41488

American (AMR) AF: 0.153 AC: 2328 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 354 AN: 3466

East Asian (EAS) AF: 0.193 AC: 994 AN: 5160

South Asian (SAS) AF: 0.221 AC: 1064 AN: 4820

European-Finnish (FIN) AF: 0.120 AC: 1257 AN: 10494

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8856 AN: 67968

Other (OTH) AF: 0.122 AC: 258 AN: 2108

Alfa AF: 0.125 Hom.: 2120

Bravo AF: 0.123

Asia WGS AF: 0.202 AC: 699 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.72
DANN	Benign	0.77
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs12041748; hg19: chr1-239224547;