1-109935442-T-C

Variant names:

• chr1-109935442-T-C
• rs756325

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 0.278 in 151,976 control chromosomes in the GnomAD database, including 7,279 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 (7279 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 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: 0.278 AC: 42244 AN: 151858 Hom.: 7269 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.278 AC: 42301 AN: 151976 Hom.: 7279 Cov.: 32 AF XY: 0.281 AC XY: 20886 AN XY: 74286

African (AFR) AF: 0.451 AC: 18670 AN: 41404

American (AMR) AF: 0.240 AC: 3660 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 419 AN: 3470

East Asian (EAS) AF: 0.627 AC: 3226 AN: 5142

South Asian (SAS) AF: 0.235 AC: 1133 AN: 4824

European-Finnish (FIN) AF: 0.206 AC: 2179 AN: 10590

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12300 AN: 67966

Other (OTH) AF: 0.233 AC: 493 AN: 2112

Alfa AF: 0.210 Hom.: 12744

Bravo AF: 0.290

Asia WGS AF: 0.439 AC: 1527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.8
DANN	Benign	0.54
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs756325; hg19: chr1-110478064; COSMIC: COSV61584007;