1-190597905-T-C

Variant names:

• chr1-190597905-T-C
• rs17379742

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 0.131 in 152,190 control chromosomes in the GnomAD database, including 1,660 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 0.13 (1660 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.189 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: 0.131 AC: 19972 AN: 152072 Hom.: 1654 Cov.: 32

Gnomad AFR AF: 0.0342

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.0977

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.131 AC: 19981 AN: 152190 Hom.: 1660 Cov.: 32 AF XY: 0.133 AC XY: 9876 AN XY: 74394

African (AFR) AF: 0.0341 AC: 1415 AN: 41546

American (AMR) AF: 0.194 AC: 2971 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3470

East Asian (EAS) AF: 0.170 AC: 877 AN: 5162

South Asian (SAS) AF: 0.0974 AC: 470 AN: 4826

European-Finnish (FIN) AF: 0.188 AC: 1989 AN: 10578

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11235 AN: 68006

Other (OTH) AF: 0.133 AC: 281 AN: 2114

Alfa AF: 0.151 Hom.: 3193

Bravo AF: 0.132

Asia WGS AF: 0.126 AC: 436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.3
DANN	Benign	0.50
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs17379742; hg19: chr1-190567035;