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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377273	XR_938873.2	n.366-310C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300096	ENST00000768769.1	n.203-310C>G		intron_variant	Intron 2 of 2
ENSG00000300096	ENST00000768770.1	n.405-310C>G		intron_variant	Intron 2 of 2
ENSG00000300096	ENST00000768771.1	n.476-310C>G		intron_variant	Intron 3 of 3
ENSG00000300096	ENST00000768772.1	n.603-310C>G		intron_variant	Intron 4 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs10518112; hg19: chr4-73863809;