1-190874079-G-T

Variant names:

• chr1-190874079-G-T
• rs1185678

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 0.0697 in 151,920 control chromosomes in the GnomAD database, including 1,064 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 0.070 (1064 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.808
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 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: 0.0697 AC: 10579 AN: 151802 Hom.: 1063 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0295

Gnomad ASJ AF: 0.00433

Gnomad EAS AF: 0.0189

Gnomad SAS AF: 0.0454

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.00641

Gnomad NFE AF: 0.00877

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0697 AC: 10594 AN: 151920 Hom.: 1064 Cov.: 32 AF XY: 0.0674 AC XY: 5008 AN XY: 74256

African (AFR) AF: 0.220 AC: 9087 AN: 41318

American (AMR) AF: 0.0295 AC: 450 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.00433 AC: 15 AN: 3468

East Asian (EAS) AF: 0.0191 AC: 99 AN: 5178

South Asian (SAS) AF: 0.0450 AC: 217 AN: 4824

European-Finnish (FIN) AF: 0.00104 AC: 11 AN: 10588

Middle Eastern (MID) AF: 0.00690 AC: 2 AN: 290

European-Non Finnish (NFE) AF: 0.00877 AC: 596 AN: 67968

Other (OTH) AF: 0.0426 AC: 90 AN: 2112

Alfa AF: 0.0530 Hom.: 122

Bravo AF: 0.0798

Asia WGS AF: 0.0360 AC: 126 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.33
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs1185678; hg19: chr1-190843209;