10-88144674-A-G

Variant names:

• chr10-88144674-A-G
• rs10509535
• ENST00000752270.1:n.382+12121A>G

Variant summary

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

The ENST00000752270.1(ENSG00000297977):​n.382+12121A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,178 control chromosomes in the GnomAD database, including 2,361 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 0.14 (2361 hom., cov: 32)
• Consequence: ENSG00000297977 ENST00000752270.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752270.1. 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	ENST00000752270.1		n.382+12121A>G		intron	N/A
	ENSG00000297977	ENST00000752272.1		n.405+12121A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21068 AN: 152060 Hom.: 2356 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0750

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0506

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0682

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.139 AC: 21093 AN: 152178 Hom.: 2361 Cov.: 32 AF XY: 0.135 AC XY: 10035 AN XY: 74404

African (AFR) AF: 0.310 AC: 12848 AN: 41484

American (AMR) AF: 0.0748 AC: 1144 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 417 AN: 3468

East Asian (EAS) AF: 0.121 AC: 624 AN: 5178

South Asian (SAS) AF: 0.111 AC: 533 AN: 4818

European-Finnish (FIN) AF: 0.0506 AC: 537 AN: 10614

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0681 AC: 4633 AN: 68000

Other (OTH) AF: 0.129 AC: 272 AN: 2112

Alfa AF: 0.0864 Hom.: 891

Bravo AF: 0.147

Asia WGS AF: 0.147 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.82
DANN	Benign	0.41
PhyloP100		-0.38

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: rs10509535;

hg19: chr10-89904431;