rs10518111

Variant names:

• chr4-72983374-G-A
• rs10518111
• ENST00000768769.1:n.118-13695G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-72983374-G-A
• chr4-72983374-G-C

Variant summary

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

The ENST00000768769.1(ENSG00000300096):​n.118-13695G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0667 in 152,212 control chromosomes in the GnomAD database, including 701 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 0.067 (701 hom., cov: 32)
• Consequence: ENSG00000300096 ENST00000768769.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 1 publications found

Genes affected

ENSG00000300096 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000768769.1. 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
	ENSG00000300096	ENST00000768769.1		n.118-13695G>A		intron	N/A
	ENSG00000300096	ENST00000768770.1		n.320-13695G>A		intron	N/A
	ENSG00000300096	ENST00000768771.1		n.390+2049G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0664 AC: 10099 AN: 152094 Hom.: 696 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.0382

Gnomad SAS AF: 0.0186

Gnomad FIN AF: 0.00988

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0154

Gnomad OTH AF: 0.0602

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

GnomAD4 genome AF: 0.0667 AC: 10148 AN: 152212 Hom.: 701 Cov.: 32 AF XY: 0.0662 AC XY: 4926 AN XY: 74436

African (AFR) AF: 0.149 AC: 6198 AN: 41486

American (AMR) AF: 0.141 AC: 2156 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0314 AC: 109 AN: 3466

East Asian (EAS) AF: 0.0383 AC: 198 AN: 5176

South Asian (SAS) AF: 0.0189 AC: 91 AN: 4824

European-Finnish (FIN) AF: 0.00988 AC: 105 AN: 10624

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0155 AC: 1051 AN: 68020

Other (OTH) AF: 0.0653 AC: 138 AN: 2114

Alfa AF: 0.0375 Hom.: 282

Bravo AF: 0.0802

Asia WGS AF: 0.0490 AC: 168 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.6
DANN	Benign	0.42
PhyloP100		-0.21

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: rs10518111;

hg19: chr4-73849091;