rs1350341

Variant names:

• chr18-60175300-G-A
• rs1350341
• ENST00000764630.1:n.798+2240C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000764630.1(ENSG00000299555):​n.798+2240C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000299555 ENST00000764630.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 13 publications found

Genes affected

ENSG00000299555 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000299555	ENST00000764630.1	n.798+2240C>T		intron_variant	Intron 1 of 2
ENSG00000299555	ENST00000764631.1	n.764-1752C>T		intron_variant	Intron 1 of 4

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

African (AFR) AF: 0.759 AC: 31496 AN: 41494

American (AMR) AF: 0.380 AC: 5788 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1140 AN: 3466

East Asian (EAS) AF: 0.219 AC: 1131 AN: 5174

South Asian (SAS) AF: 0.555 AC: 2675 AN: 4822

European-Finnish (FIN) AF: 0.429 AC: 4520 AN: 10532

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29723 AN: 67940

Other (OTH) AF: 0.470 AC: 993 AN: 2112

Alfa AF: 0.462 Hom.: 8989

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1350341; hg19: chr18-57842533;