ENST00000722712.1:n.269-39964T>C

Variant names:

• chr5-63737891-A-G
• rs10042968
• ENST00000722712.1:n.269-39964T>C

Variant summary

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

The ENST00000722712.1(ENSG00000294317):​n.269-39964T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,052 control chromosomes in the GnomAD database, including 3,308 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 0.20 (3308 hom., cov: 33)
• Consequence: ENSG00000294317 ENST00000722712.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65
• Publications: 7 publications found

Genes affected

ENSG00000294317 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722712.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294317	ENST00000722712.1		n.269-39964T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30682 AN: 151934 Hom.: 3307 Cov.: 33

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0226

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.202 AC: 30695 AN: 152052 Hom.: 3308 Cov.: 33 AF XY: 0.197 AC XY: 14670 AN XY: 74344

African (AFR) AF: 0.241 AC: 10020 AN: 41496

American (AMR) AF: 0.175 AC: 2665 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 726 AN: 3470

East Asian (EAS) AF: 0.0227 AC: 117 AN: 5156

South Asian (SAS) AF: 0.103 AC: 497 AN: 4828

European-Finnish (FIN) AF: 0.158 AC: 1677 AN: 10608

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14276 AN: 67936

Other (OTH) AF: 0.203 AC: 428 AN: 2112

Alfa AF: 0.206 Hom.: 5459

Bravo AF: 0.207

Asia WGS AF: 0.0720 AC: 253 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	16
DANN	Benign	0.78
PhyloP100		1.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10042968; hg19: chr5-63033718;