rs4791872

Variant names:

• chr17-9799908-A-G
• rs4791872
• ENST00000609065.1:n.138+7582T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000609065.1(ENSG00000278944):​n.138+7582T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0541 in 152,244 control chromosomes in the GnomAD database, including 1,099 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 0.054 (1099 hom., cov: 32)
• Consequence: ENSG00000278944 ENST00000609065.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.450

Genes affected

ENSG00000278944 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000278944	ENST00000609065.1	n.138+7582T>C		intron_variant	Intron 2 of 2	5
ENSG00000282882	ENST00000634974.2	n.283-3875A>G		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.0539 AC: 8194 AN: 152126 Hom.: 1087 Cov.: 32

Gnomad AFR AF: 0.0108

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.0429

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.0663

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00785

Gnomad OTH AF: 0.0549

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

GnomAD4 genome AF: 0.0541 AC: 8229 AN: 152244 Hom.: 1099 Cov.: 32 AF XY: 0.0645 AC XY: 4802 AN XY: 74438

Gnomad4 AFR AF: 0.0107

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.0429

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.0663

Gnomad4 NFE AF: 0.00785

Gnomad4 OTH AF: 0.0610

Alfa AF: 0.0356 Hom.: 140

Bravo AF: 0.0631

Asia WGS AF: 0.303 AC: 1052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.21
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4791872; hg19: chr17-9703225;