10-57384335-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812047.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305625	ENST00000812047.1		n.76-19505C>A		intron	N/A
	ENSG00000305625	ENST00000812048.1		n.63-8229C>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1904764;

hg19: chr10-59144095;