1-118360355-A-G

Variant names:

• chr1-118360355-A-G
• rs2474937

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 0.242 in 151,610 control chromosomes in the GnomAD database, including 4,782 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 0.24 (4782 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 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: 0.242 AC: 36620 AN: 151492 Hom.: 4775 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0734

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.242 AC: 36670 AN: 151610 Hom.: 4782 Cov.: 32 AF XY: 0.238 AC XY: 17667 AN XY: 74138

African (AFR) AF: 0.333 AC: 13807 AN: 41418

American (AMR) AF: 0.212 AC: 3222 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 651 AN: 3460

East Asian (EAS) AF: 0.0730 AC: 377 AN: 5162

South Asian (SAS) AF: 0.266 AC: 1282 AN: 4822

European-Finnish (FIN) AF: 0.185 AC: 1954 AN: 10572

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14527 AN: 67690

Other (OTH) AF: 0.240 AC: 505 AN: 2102

Alfa AF: 0.221 Hom.: 17075

Bravo AF: 0.247

Asia WGS AF: 0.176 AC: 615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.44
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs2474937; hg19: chr1-118902978;