rs10042348

Variant names:

• chr5-51922017-C-G
• rs10042348
• ENST00000771174.1:n.694+15685G>C

Variant summary

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

The ENST00000771174.1(ENSG00000300361):​n.694+15685G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 151,926 control chromosomes in the GnomAD database, including 37,027 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 0.67 (37027 hom., cov: 30)
• Consequence: ENSG00000300361 ENST00000771174.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803
• Publications: 5 publications found

Genes affected

ENSG00000300361 (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 (NFE) allele frequency at 95% confidence interval = 0.806 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
ENSG00000300361	ENST00000771174.1	n.694+15685G>C		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101365 AN: 151810 Hom.: 37025 Cov.: 30

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.803

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.667 AC: 101382 AN: 151926 Hom.: 37027 Cov.: 30 AF XY: 0.671 AC XY: 49840 AN XY: 74278

African (AFR) AF: 0.358 AC: 14825 AN: 41418

American (AMR) AF: 0.743 AC: 11328 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2887 AN: 3466

East Asian (EAS) AF: 0.462 AC: 2377 AN: 5140

South Asian (SAS) AF: 0.773 AC: 3718 AN: 4812

European-Finnish (FIN) AF: 0.823 AC: 8690 AN: 10556

Middle Eastern (MID) AF: 0.791 AC: 231 AN: 292

European-Non Finnish (NFE) AF: 0.812 AC: 55179 AN: 67968

Other (OTH) AF: 0.710 AC: 1495 AN: 2106

Alfa AF: 0.731 Hom.: 5341

Bravo AF: 0.646

Asia WGS AF: 0.621 AC: 2160 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	0.18
DANN	Benign	0.70
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs10042348; hg19: chr5-51217851;