1-119397758-T-G

Variant names:

• chr1-119397758-T-G
• rs2005390

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 0.662 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.662 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

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.631

Alfa AF: 0.620 Hom.: 11736

Bravo AF: 0.667

Asia WGS AF: 0.652 AC: 2270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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