rs4795541

Variant names:

• chr17-30237299-A-G
• rs4795541
• ENST00000724731.1:n.109+229A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000724731.1(ENSG00000266120):​n.109+229A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0011 (0 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000266120 ENST00000724731.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.910
• Publications: 68 publications found

Genes affected

ENSG00000266120 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371720	XR_001752824.2	n.280+229A>G		intron_variant	Intron 1 of 3
LOC105371720	XR_007065695.1	n.-199A>G		upstream_gene_variant
LOC105371720	XR_007065696.1	n.-199A>G		upstream_gene_variant
LOC105371720	XR_007065698.1	n.-199A>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000266120	ENST00000724731.1	n.109+229A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.00108 AC: 13 AN: 12010 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000733

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00134

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0109

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00216

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00118

Gnomad OTH AF: 0.00

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00108 AC: 13 AN: 12024 Hom.: 0 Cov.: 0 AF XY: 0.00110 AC XY: 6 AN XY: 5438

African (AFR) AF: 0.000731 AC: 3 AN: 4102

American (AMR) AF: 0.00134 AC: 1 AN: 748

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 262

East Asian (EAS) AF: 0.0111 AC: 1 AN: 90

South Asian (SAS) AF: 0.00 AC: 0 AN: 178

European-Finnish (FIN) AF: 0.00216 AC: 1 AN: 462

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 16

European-Non Finnish (NFE) AF: 0.00118 AC: 7 AN: 5954

Other (OTH) AF: 0.00 AC: 0 AN: 116

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	2.2
DANN	Benign	0.34
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs4795541; hg19: chr17-28564317;