rs9630112

Variant names:

• chr10-88084818-T-A
• rs9630112
• ENST00000752267.1:n.648+23388T>A

Your query was ambiguous. Multiple possible variants found:

• chr10-88084818-T-A
• chr10-88084818-T-C
• chr10-88084818-T-G

Variant summary

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

The ENST00000752267.1(ENSG00000297977):​n.648+23388T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 152,062 control chromosomes in the GnomAD database, including 22,800 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 0.52 (22800 hom., cov: 32)
• Consequence: ENSG00000297977 ENST00000752267.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303
• Publications: 0 publications found

Genes affected

ENSG00000297977 (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 (AFR) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378415	XR_007062225.1	n.264+431A>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297977	ENST00000752267.1	n.648+23388T>A		intron_variant	Intron 4 of 4
ENSG00000297977	ENST00000752268.1	n.674+15176T>A		intron_variant	Intron 5 of 5
ENSG00000297977	ENST00000752271.1	n.262+17965T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78790 AN: 151942 Hom.: 22759 Cov.: 32

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.519 AC: 78883 AN: 152062 Hom.: 22800 Cov.: 32 AF XY: 0.511 AC XY: 38017 AN XY: 74342

African (AFR) AF: 0.791 AC: 32807 AN: 41460

American (AMR) AF: 0.454 AC: 6939 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1585 AN: 3468

East Asian (EAS) AF: 0.158 AC: 820 AN: 5182

South Asian (SAS) AF: 0.471 AC: 2270 AN: 4824

European-Finnish (FIN) AF: 0.421 AC: 4445 AN: 10568

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28382 AN: 67966

Other (OTH) AF: 0.527 AC: 1111 AN: 2108

Alfa AF: 0.265 Hom.: 533

Bravo AF: 0.532

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.083
DANN	Benign	0.78
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs9630112; hg19: chr10-89844575;