rs1350341

Variant names:

• chr18-60175300-G-A
• rs1350341

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 0.513 in 151,988 control chromosomes in the GnomAD database, including 22,087 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 0.51 (22087 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.752 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: 0.513 AC: 77902 AN: 151870 Hom.: 22046 Cov.: 32

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.513 AC: 77995 AN: 151988 Hom.: 22087 Cov.: 32 AF XY: 0.508 AC XY: 37720 AN XY: 74268

Gnomad4 AFR AF: 0.759

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.470

Alfa AF: 0.462 Hom.: 7999

Bravo AF: 0.515

Asia WGS AF: 0.393 AC: 1365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1350341; hg19: chr18-57842533;