chr1-190534836-C-T

Variant names:

• chr1-190534836-C-T
• rs755805

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 0.114 in 151,408 control chromosomes in the GnomAD database, including 1,291 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 0.11 (1291 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.203 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: 0.114 AC: 17190 AN: 151288 Hom.: 1275 Cov.: 32

Gnomad AFR AF: 0.0329

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.0812

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0639

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.114 AC: 17224 AN: 151408 Hom.: 1291 Cov.: 32 AF XY: 0.115 AC XY: 8492 AN XY: 73948

Gnomad4 AFR AF: 0.0328

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.0812

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.0637

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.125

Alfa AF: 0.132 Hom.: 1974

Bravo AF: 0.119

Asia WGS AF: 0.137 AC: 476 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs755805; hg19: chr1-190503966;