1-114173741-C-T

Variant names:

• chr1-114173741-C-T
• rs6657718

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 0.21 in 152,014 control chromosomes in the GnomAD database, including 3,662 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 0.21 (3662 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 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: 0.210 AC: 31897 AN: 151896 Hom.: 3662 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0812

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.210 AC: 31909 AN: 152014 Hom.: 3662 Cov.: 32 AF XY: 0.202 AC XY: 15022 AN XY: 74312

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.00289

Gnomad4 SAS AF: 0.0806

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.214

Alfa AF: 0.204 Hom.: 1877

Bravo AF: 0.211

Asia WGS AF: 0.0560 AC: 196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.014
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6657718; hg19: chr1-114716363;