rs2145418

Variant names:

• chr1-118422631-C-A
• rs2145418

Your query was ambiguous. Multiple possible variants found:

• chr1-118422631-C-A
• chr1-118422631-C-G
• chr1-118422631-C-T

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 0.777 in 152,112 control chromosomes in the GnomAD database, including 46,334 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 0.78 (46334 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.801
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.828 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: 0.777 AC: 118087 AN: 151994 Hom.: 46316 Cov.: 31

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.768

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.777 AC: 118142 AN: 152112 Hom.: 46334 Cov.: 31 AF XY: 0.777 AC XY: 57817 AN XY: 74364

African (AFR) AF: 0.699 AC: 28977 AN: 41478

American (AMR) AF: 0.682 AC: 10426 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 2499 AN: 3468

East Asian (EAS) AF: 0.703 AC: 3624 AN: 5154

South Asian (SAS) AF: 0.828 AC: 3983 AN: 4810

European-Finnish (FIN) AF: 0.888 AC: 9398 AN: 10584

Middle Eastern (MID) AF: 0.784 AC: 229 AN: 292

European-Non Finnish (NFE) AF: 0.833 AC: 56675 AN: 68010

Other (OTH) AF: 0.763 AC: 1611 AN: 2112

Alfa AF: 0.794 Hom.: 17315

Bravo AF: 0.754

Asia WGS AF: 0.750 AC: 2612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.84
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs2145418; hg19: chr1-118965254;