rs17876205

Variant names:

• chr7-95403792-C-G
• rs17876205
• ENST00000718462.1:n.589+6764C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000718462.1(ENSG00000233942):​n.589+6764C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 152,274 control chromosomes in the GnomAD database, including 35 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 0.014 (35 hom., cov: 33)
• Consequence: ENSG00000233942 ENST00000718462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249
• Publications: 1 publications found

Genes affected

ENSG00000233942 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0141 (2150/152274) while in subpopulation SAS AF = 0.0404 (195/4824). AF 95% confidence interval is 0.0358. There are 35 homozygotes in GnomAd4. There are 1231 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 35 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718462.1. 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
	ENSG00000233942	ENST00000718462.1		n.589+6764C>G		intron	N/A
	ENSG00000233942	ENST00000818771.1		n.521+6764C>G		intron	N/A
	ENSG00000233942	ENST00000818772.1		n.463+6764C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0141 AC: 2152 AN: 152156 Hom.: 35 Cov.: 33

Gnomad AFR AF: 0.00198

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0115

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0402

Gnomad FIN AF: 0.0478

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0157

Gnomad OTH AF: 0.0153

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

GnomAD4 genome AF: 0.0141 AC: 2150 AN: 152274 Hom.: 35 Cov.: 33 AF XY: 0.0165 AC XY: 1231 AN XY: 74446

African (AFR) AF: 0.00197 AC: 82 AN: 41550

American (AMR) AF: 0.0115 AC: 176 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3470

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.0404 AC: 195 AN: 4824

European-Finnish (FIN) AF: 0.0478 AC: 507 AN: 10600

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0157 AC: 1071 AN: 68018

Other (OTH) AF: 0.0151 AC: 32 AN: 2114

Alfa AF: 0.0170 Hom.: 3

Bravo AF: 0.0103

Asia WGS AF: 0.0110 AC: 39 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.58
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs17876205; hg19: chr7-95033104;