rs618171

Variant names:

• chr1-218975956-A-G
• rs618171

Your query was ambiguous. Multiple possible variants found:

• chr1-218975956-A-G
• chr1-218975956-A-T

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 0.576 in 152,074 control chromosomes in the GnomAD database, including 28,685 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 0.58 (28685 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.727 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: 0.576 AC: 87545 AN: 151956 Hom.: 28687 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.576 AC: 87560 AN: 152074 Hom.: 28685 Cov.: 32 AF XY: 0.578 AC XY: 42936 AN XY: 74342

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.818

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.584

Alfa AF: 0.689 Hom.: 45706

Bravo AF: 0.544

Asia WGS AF: 0.501 AC: 1743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs618171; hg19: chr1-219149298;