chr10-43072898-G-C

Variant names:

• chr10-43072898-G-C
• rs741763
• ENST00000794440.1:n.52-1387C>G

Variant summary

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

The ENST00000794440.1(ENSG00000303432):​n.52-1387C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,964 control chromosomes in the GnomAD database, including 10,056 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 0.36 (10056 hom., cov: 32)
• Consequence: ENSG00000303432 ENST00000794440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• Publications: 3 publications found

Genes affected

ENSG00000303432 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794440.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303432	ENST00000794440.1		n.52-1387C>G		intron	N/A
	ENSG00000303432	ENST00000794441.1		n.117-1387C>G		intron	N/A
	ENSG00000303432	ENST00000794442.1		n.108-1387C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54085 AN: 151846 Hom.: 10035 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.356 AC: 54131 AN: 151964 Hom.: 10056 Cov.: 32 AF XY: 0.357 AC XY: 26519 AN XY: 74278

African (AFR) AF: 0.246 AC: 10219 AN: 41476

American (AMR) AF: 0.408 AC: 6232 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1149 AN: 3468

East Asian (EAS) AF: 0.317 AC: 1630 AN: 5144

South Asian (SAS) AF: 0.421 AC: 2017 AN: 4790

European-Finnish (FIN) AF: 0.373 AC: 3950 AN: 10578

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27621 AN: 67928

Other (OTH) AF: 0.358 AC: 754 AN: 2104

Alfa AF: 0.361 Hom.: 1264

Bravo AF: 0.354

Asia WGS AF: 0.358 AC: 1244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.1
DANN	Benign	0.72
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs741763; hg19: chr10-43568346;