ENST00000782972.1:n.18+926T>C

Variant names:

• chr4-183356154-A-G
• rs17074631
• ENST00000782972.1:n.18+926T>C

Variant summary

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

The ENST00000782972.1(ENSG00000301933):​n.18+926T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,170 control chromosomes in the GnomAD database, including 919 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 0.10 (919 hom., cov: 32)
• Consequence: ENSG00000301933 ENST00000782972.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• Publications: 2 publications found

Genes affected

ENSG00000301933 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782972.1. 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
	ENSG00000301933	ENST00000782972.1		n.18+926T>C		intron	N/A
	ENSG00000301954	ENST00000783051.1		n.181-802A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15897 AN: 152052 Hom.: 914 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.0703

Gnomad ASJ AF: 0.0291

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.0492

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0981

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

GnomAD4 genome AF: 0.105 AC: 15928 AN: 152170 Hom.: 919 Cov.: 32 AF XY: 0.103 AC XY: 7685 AN XY: 74396

African (AFR) AF: 0.113 AC: 4684 AN: 41504

American (AMR) AF: 0.0705 AC: 1078 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0291 AC: 101 AN: 3468

East Asian (EAS) AF: 0.0110 AC: 57 AN: 5172

South Asian (SAS) AF: 0.0490 AC: 236 AN: 4814

European-Finnish (FIN) AF: 0.139 AC: 1472 AN: 10596

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7935 AN: 68004

Other (OTH) AF: 0.0980 AC: 207 AN: 2112

Alfa AF: 0.105 Hom.: 1460

Bravo AF: 0.0985

Asia WGS AF: 0.0480 AC: 167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.2
DANN	Benign	0.46
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs17074631; hg19: chr4-184277307;