rs1904444

Variant names:

• chr10-113317597-G-A
• rs1904444
• ENST00000818152.1:n.270-39424G>A

Variant summary

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

The ENST00000818152.1(ENSG00000306410):​n.270-39424G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,214 control chromosomes in the GnomAD database, including 1,828 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 0.13 (1828 hom., cov: 33)
• Consequence: ENSG00000306410 ENST00000818152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 4 publications found

Genes affected

ENSG00000306410 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378490	XR_946329.2	n.4888-3207G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306410	ENST00000818152.1	n.270-39424G>A		intron_variant	Intron 1 of 1
ENSG00000306410	ENST00000818153.1	n.125-39424G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20067 AN: 152096 Hom.: 1826 Cov.: 33

Gnomad AFR AF: 0.0325

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.132 AC: 20070 AN: 152214 Hom.: 1828 Cov.: 33 AF XY: 0.135 AC XY: 10068 AN XY: 74412

African (AFR) AF: 0.0325 AC: 1349 AN: 41558

American (AMR) AF: 0.222 AC: 3388 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 566 AN: 3472

East Asian (EAS) AF: 0.360 AC: 1862 AN: 5170

South Asian (SAS) AF: 0.193 AC: 932 AN: 4824

European-Finnish (FIN) AF: 0.125 AC: 1320 AN: 10584

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10219 AN: 68012

Other (OTH) AF: 0.135 AC: 286 AN: 2112

Alfa AF: 0.145 Hom.: 4531

Bravo AF: 0.137

Asia WGS AF: 0.229 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
DANN	Benign	0.51
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1904444; hg19: chr10-115077356;