1-146040040-G-T

Variant names:

• chr1-146040040-G-T
• rs10797649

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 0.368 in 152,000 control chromosomes in the GnomAD database, including 11,964 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 0.37 (11964 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55945 AN: 151884 Hom.: 11962 Cov.: 31

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.368 AC: 55958 AN: 152000 Hom.: 11964 Cov.: 31 AF XY: 0.370 AC XY: 27512 AN XY: 74282

African (AFR) AF: 0.145 AC: 6013 AN: 41480

American (AMR) AF: 0.364 AC: 5562 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1510 AN: 3470

East Asian (EAS) AF: 0.425 AC: 2195 AN: 5168

South Asian (SAS) AF: 0.476 AC: 2294 AN: 4816

European-Finnish (FIN) AF: 0.469 AC: 4948 AN: 10540

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32207 AN: 67948

Other (OTH) AF: 0.373 AC: 788 AN: 2114

Alfa AF: 0.437 Hom.: 60719

Bravo AF: 0.347

Asia WGS AF: 0.425 AC: 1474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.4
DANN	Benign	0.37
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs10797649; hg19: chr1-145394955;