4-72998092-C-G

Variant names:

• chr4-72998092-C-G
• rs10518112
• ENST00000768769.1:n.203-310C>G

Variant summary

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

The ENST00000768769.1(ENSG00000300096):​n.203-310C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,120 control chromosomes in the GnomAD database, including 2,125 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 0.16 (2125 hom., cov: 32)
• Consequence: ENSG00000300096 ENST00000768769.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 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.203-310C>G		intron	N/A
	ENSG00000300096	ENST00000768770.1		n.405-310C>G		intron	N/A
	ENSG00000300096	ENST00000768771.1		n.476-310C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24022 AN: 152002 Hom.: 2115 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.158 AC: 24059 AN: 152120 Hom.: 2125 Cov.: 32 AF XY: 0.158 AC XY: 11760 AN XY: 74368

African (AFR) AF: 0.219 AC: 9080 AN: 41482

American (AMR) AF: 0.144 AC: 2197 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 810 AN: 3470

East Asian (EAS) AF: 0.133 AC: 689 AN: 5168

South Asian (SAS) AF: 0.211 AC: 1019 AN: 4826

European-Finnish (FIN) AF: 0.113 AC: 1201 AN: 10590

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.126 AC: 8587 AN: 68002

Other (OTH) AF: 0.163 AC: 343 AN: 2108

Alfa AF: 0.0501 Hom.: 39

Bravo AF: 0.165

Asia WGS AF: 0.194 AC: 676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.57
DANN	Benign	0.28
PhyloP100		-0.69

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: rs10518112;

hg19: chr4-73863809;