1-118881404-T-A

Position:

• chr1-118881404-T-A

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 0.11 in 152,264 control chromosomes in the GnomAD database, including 1,172 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 (1172 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16679 AN: 152146 Hom.: 1171 Cov.: 33

Gnomad AFR AF: 0.0305

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.0968

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.110 AC: 16677 AN: 152264 Hom.: 1172 Cov.: 33 AF XY: 0.111 AC XY: 8236 AN XY: 74436

Gnomad4 AFR AF: 0.0304

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.0968

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.127

Alfa AF: 0.120 Hom.: 132

Bravo AF: 0.104

Asia WGS AF: 0.236 AC: 820 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6680654; hg19: chr1-119424027;