1-190097256-T-C

Variant names:

• chr1-190097256-T-C
• rs1935881

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 0.281 in 152,052 control chromosomes in the GnomAD database, including 6,546 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 0.28 (6546 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.352 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: 0.281 AC: 42747 AN: 151934 Hom.: 6543 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.281 AC: 42760 AN: 152052 Hom.: 6546 Cov.: 32 AF XY: 0.278 AC XY: 20697 AN XY: 74326

African (AFR) AF: 0.173 AC: 7191 AN: 41498

American (AMR) AF: 0.218 AC: 3325 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1163 AN: 3472

East Asian (EAS) AF: 0.114 AC: 588 AN: 5176

South Asian (SAS) AF: 0.284 AC: 1370 AN: 4818

European-Finnish (FIN) AF: 0.366 AC: 3871 AN: 10564

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.355 AC: 24145 AN: 67944

Other (OTH) AF: 0.279 AC: 589 AN: 2108

Alfa AF: 0.322 Hom.: 23433

Bravo AF: 0.264

Asia WGS AF: 0.199 AC: 690 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.089
DANN	Benign	0.55
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1935881; hg19: chr1-190066386;