rs10484042

Variant names:

• chr14-94397364-G-A
• rs10484042
• ENST00000693506.1:n.124+6470G>A

Variant summary

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

The ENST00000693506.1(ENSG00000256357):​n.124+6470G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0472 in 152,170 control chromosomes in the GnomAD database, including 388 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 0.047 (388 hom., cov: 33)
• Consequence: ENSG00000256357 ENST00000693506.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 3 publications found

Genes affected

ENSG00000256357 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.164 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
ENSG00000256357	ENST00000693506.1	n.124+6470G>A		intron_variant	Intron 1 of 1
ENSG00000256357	ENST00000811346.1	n.227+7499G>A		intron_variant	Intron 1 of 2
ENSG00000256357	ENST00000811347.1	n.208+7499G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0472 AC: 7171 AN: 152052 Hom.: 385 Cov.: 33

Gnomad AFR AF: 0.0116

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0279

Gnomad EAS AF: 0.00520

Gnomad SAS AF: 0.0915

Gnomad FIN AF: 0.0279

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0460

Gnomad OTH AF: 0.0426

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

GnomAD4 genome AF: 0.0472 AC: 7184 AN: 152170 Hom.: 388 Cov.: 33 AF XY: 0.0510 AC XY: 3793 AN XY: 74392

African (AFR) AF: 0.0116 AC: 481 AN: 41520

American (AMR) AF: 0.170 AC: 2589 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0279 AC: 97 AN: 3472

East Asian (EAS) AF: 0.00502 AC: 26 AN: 5178

South Asian (SAS) AF: 0.0918 AC: 443 AN: 4824

European-Finnish (FIN) AF: 0.0279 AC: 296 AN: 10592

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0460 AC: 3126 AN: 67996

Other (OTH) AF: 0.0422 AC: 89 AN: 2110

Alfa AF: 0.0445 Hom.: 237

Bravo AF: 0.0539

Asia WGS AF: 0.0570 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.77
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10484042; hg19: chr14-94863701;