rs732610

Variant names:

• chr10-43072623-C-G
• rs732610
• ENST00000794440.1:n.52-1112G>C

Your query was ambiguous. Multiple possible variants found:

• chr10-43072623-C-G
• chr10-43072623-C-T

Variant summary

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

The ENST00000794440.1(ENSG00000303432):​n.52-1112G>C 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 152,006 control chromosomes in the GnomAD database, including 10,046 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 (10046 hom., cov: 32)
• Consequence: ENSG00000303432 ENST00000794440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.761
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 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
ENSG00000303432	ENST00000794440.1	n.52-1112G>C		intron_variant	Intron 1 of 2
ENSG00000303432	ENST00000794441.1	n.117-1112G>C		intron_variant	Intron 1 of 3
ENSG00000303432	ENST00000794442.1	n.108-1112G>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54068 AN: 151890 Hom.: 10026 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.406

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: 54112 AN: 152006 Hom.: 10046 Cov.: 32 AF XY: 0.357 AC XY: 26512 AN XY: 74296

African (AFR) AF: 0.246 AC: 10211 AN: 41448

American (AMR) AF: 0.408 AC: 6240 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1149 AN: 3470

East Asian (EAS) AF: 0.317 AC: 1629 AN: 5146

South Asian (SAS) AF: 0.422 AC: 2030 AN: 4814

European-Finnish (FIN) AF: 0.373 AC: 3947 AN: 10570

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

European-Non Finnish (NFE) AF: 0.406 AC: 27593 AN: 67958

Other (OTH) AF: 0.358 AC: 756 AN: 2110

Alfa AF: 0.368 Hom.: 1326

Bravo AF: 0.354

Asia WGS AF: 0.359 AC: 1245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.54
DANN	Benign	0.64
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs732610; hg19: chr10-43568071;