10-111562003-T-C

Variant names:

• chr10-111562003-T-C
• rs1878248
• ENST00000829409.1:n.117-60327A>G

Variant summary

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

The ENST00000829409.1(ENSG00000307856):​n.117-60327A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 152,154 control chromosomes in the GnomAD database, including 43,935 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 0.75 (43935 hom., cov: 32)
• Consequence: ENSG00000307856 ENST00000829409.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377
• Publications: 1 publications found

Genes affected

ENSG00000307856 (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 = 0.901 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829409.1. 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
	ENSG00000307856	ENST00000829409.1		n.117-60327A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114312 AN: 152038 Hom.: 43896 Cov.: 32

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.752 AC: 114402 AN: 152154 Hom.: 43935 Cov.: 32 AF XY: 0.750 AC XY: 55805 AN XY: 74380

African (AFR) AF: 0.908 AC: 37723 AN: 41530

American (AMR) AF: 0.588 AC: 8985 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2632 AN: 3470

East Asian (EAS) AF: 0.587 AC: 3022 AN: 5144

South Asian (SAS) AF: 0.725 AC: 3496 AN: 4824

European-Finnish (FIN) AF: 0.768 AC: 8135 AN: 10586

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48105 AN: 67998

Other (OTH) AF: 0.730 AC: 1544 AN: 2114

Alfa AF: 0.722 Hom.: 28842

Bravo AF: 0.741

Asia WGS AF: 0.679 AC: 2365 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	2.2
DANN	Benign	0.52
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: rs1878248;

hg19: chr10-113321761;