rs1518350

Variant names:

• chr6-117878274-C-A
• rs1518350

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 0.277 in 151,866 control chromosomes in the GnomAD database, including 5,980 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 0.28 (5980 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.332 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: 0.278 AC: 42111 AN: 151750 Hom.: 5979 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.277 AC: 42130 AN: 151866 Hom.: 5980 Cov.: 32 AF XY: 0.278 AC XY: 20597 AN XY: 74176

African (AFR) AF: 0.287 AC: 11873 AN: 41422

American (AMR) AF: 0.339 AC: 5177 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 987 AN: 3468

East Asian (EAS) AF: 0.174 AC: 901 AN: 5166

South Asian (SAS) AF: 0.251 AC: 1208 AN: 4804

European-Finnish (FIN) AF: 0.266 AC: 2798 AN: 10502

Middle Eastern (MID) AF: 0.372 AC: 108 AN: 290

European-Non Finnish (NFE) AF: 0.269 AC: 18263 AN: 67940

Other (OTH) AF: 0.315 AC: 664 AN: 2110

Alfa AF: 0.277 Hom.: 1436

Bravo AF: 0.285

Asia WGS AF: 0.199 AC: 691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.8
DANN	Benign	0.54
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs1518350; hg19: chr6-118199437;