chr1-117581356-T-C

Variant names:

• chr1-117581356-T-C
• rs861153

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 0.492 in 152,102 control chromosomes in the GnomAD database, including 18,861 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 0.49 (18861 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.958

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 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: 0.492 AC: 74811 AN: 151984 Hom.: 18835 Cov.: 32

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.492 AC: 74886 AN: 152102 Hom.: 18861 Cov.: 32 AF XY: 0.489 AC XY: 36363 AN XY: 74352

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.459

Alfa AF: 0.456 Hom.: 8226

Bravo AF: 0.499

Asia WGS AF: 0.578 AC: 2007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs861153; hg19: chr1-118123978;