1-119397758-T-G

Variant names:

• chr1-119397758-T-G
• rs2005390

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 0.662 in 151,966 control chromosomes in the GnomAD database, including 33,462 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 0.66 (33462 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.702 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: 0.662 AC: 100491 AN: 151846 Hom.: 33428 Cov.: 32

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.662 AC: 100579 AN: 151966 Hom.: 33462 Cov.: 32 AF XY: 0.664 AC XY: 49352 AN XY: 74272

African (AFR) AF: 0.709 AC: 29394 AN: 41448

American (AMR) AF: 0.700 AC: 10686 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1896 AN: 3470

East Asian (EAS) AF: 0.698 AC: 3598 AN: 5154

South Asian (SAS) AF: 0.630 AC: 3036 AN: 4820

European-Finnish (FIN) AF: 0.664 AC: 7016 AN: 10562

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42691 AN: 67932

Other (OTH) AF: 0.631 AC: 1330 AN: 2108

Alfa AF: 0.623 Hom.: 13535

Bravo AF: 0.667

Asia WGS AF: 0.652 AC: 2270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.84
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2005390; hg19: chr1-119940381; COSMIC: COSV58038702;