rs861153

Variant names:

• chr1-117581356-T-C
• rs861153

Your query was ambiguous. Multiple possible variants found:

• chr1-117581356-T-C
• chr1-117581356-T-G

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 0.492 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.591 AC: 24540 AN: 41488

American (AMR) AF: 0.473 AC: 7229 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1187 AN: 3470

East Asian (EAS) AF: 0.651 AC: 3365 AN: 5166

South Asian (SAS) AF: 0.451 AC: 2174 AN: 4822

European-Finnish (FIN) AF: 0.424 AC: 4483 AN: 10564

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30282 AN: 67990

Other (OTH) AF: 0.459 AC: 967 AN: 2108

Alfa AF: 0.475 Hom.: 14271

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
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs861153; hg19: chr1-118123978;