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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752267.1. 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
	ENSG00000297977	ENST00000752267.1		n.648+23388T>A		intron	N/A
	ENSG00000297977	ENST00000752268.1		n.674+15176T>A		intron	N/A
	ENSG00000297977	ENST00000752271.1		n.262+17965T>A		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs9630112;

hg19: chr10-89844575;