chr10-57384335-G-T

Variant names:

• chr10-57384335-G-T
• rs1904764
• ENST00000812047.1:n.76-19505C>A

Variant summary

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

The ENST00000812047.1(ENSG00000305625):​n.76-19505C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,034 control chromosomes in the GnomAD database, including 4,700 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 0.24 (4700 hom., cov: 32)
• Consequence: ENSG00000305625 ENST00000812047.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 4 publications found

Genes affected

ENSG00000305625 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378313	XR_001747453.1	n.63-8229C>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305625	ENST00000812047.1	n.76-19505C>A		intron_variant	Intron 2 of 2
ENSG00000305625	ENST00000812048.1	n.63-8229C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35747 AN: 151918 Hom.: 4700 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.00618

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.235 AC: 35753 AN: 152034 Hom.: 4700 Cov.: 32 AF XY: 0.232 AC XY: 17245 AN XY: 74342

African (AFR) AF: 0.163 AC: 6767 AN: 41492

American (AMR) AF: 0.215 AC: 3275 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1043 AN: 3470

East Asian (EAS) AF: 0.00600 AC: 31 AN: 5170

South Asian (SAS) AF: 0.256 AC: 1232 AN: 4814

European-Finnish (FIN) AF: 0.233 AC: 2467 AN: 10568

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20034 AN: 67946

Other (OTH) AF: 0.262 AC: 550 AN: 2100

Alfa AF: 0.269 Hom.: 7361

Bravo AF: 0.230

Asia WGS AF: 0.129 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.42
DANN	Benign	0.66
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1904764; hg19: chr10-59144095;