rs4791872

chr17-9799908-A-G

Variant summary

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

The ENST00000634974.2(ENSG00000282882):n.283-3875A>G variant causes a intron, non coding transcript 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: ENST00000634974.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.450

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000634974.2	n.283-3875A>G		intron_variant, non_coding_transcript_variant		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;