rs717698

Variant names:

• chr7-8354618-G-A
• rs717698
• ENST00000741032.1:n.293G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-8354618-G-A
• chr7-8354618-G-C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000741032.1(ENSG00000296655):​n.293G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 152,114 control chromosomes in the GnomAD database, including 29,941 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 0.61 (29941 hom., cov: 33)
• Consequence: ENSG00000296655 ENST00000741032.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317
• Publications: 3 publications found

Genes affected

ENSG00000296655 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.833 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
ENSG00000296655	ENST00000741032.1	n.293G>A		non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000296655	ENST00000741033.1	n.296G>A		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000296655	ENST00000741034.1	n.336G>A		non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.612 AC: 93016 AN: 151996 Hom.: 29897 Cov.: 33

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.612 AC: 93107 AN: 152114 Hom.: 29941 Cov.: 33 AF XY: 0.609 AC XY: 45267 AN XY: 74338

African (AFR) AF: 0.800 AC: 33207 AN: 41504

American (AMR) AF: 0.542 AC: 8278 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2226 AN: 3470

East Asian (EAS) AF: 0.854 AC: 4427 AN: 5186

South Asian (SAS) AF: 0.634 AC: 3057 AN: 4820

European-Finnish (FIN) AF: 0.418 AC: 4409 AN: 10550

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.522 AC: 35460 AN: 67982

Other (OTH) AF: 0.581 AC: 1227 AN: 2112

Alfa AF: 0.568 Hom.: 49065

Bravo AF: 0.628

Asia WGS AF: 0.728 AC: 2531 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	17
DANN	Benign	0.52
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs717698; hg19: chr7-8394248;