rs17706620

Variant names:

• chr7-41878941-T-C
• rs17706620
• ENST00000840521.1:n.139T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000840521.1(ENSG00000309360):​n.139T>C 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 0.313 in 152,154 control chromosomes in the GnomAD database, including 8,862 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 0.31 (8862 hom., cov: 32)
• Consequence: ENSG00000309360 ENST00000840521.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.676
• Publications: 2 publications found

Genes affected

ENSG00000309360 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000840521.1. 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
	ENSG00000309360	ENST00000840521.1		n.139T>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000309263	ENST00000839902.1		n.566+6820T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47667 AN: 152036 Hom.: 8855 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.313 AC: 47687 AN: 152154 Hom.: 8862 Cov.: 32 AF XY: 0.315 AC XY: 23450 AN XY: 74354

African (AFR) AF: 0.130 AC: 5392 AN: 41546

American (AMR) AF: 0.251 AC: 3830 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1482 AN: 3472

East Asian (EAS) AF: 0.189 AC: 979 AN: 5182

South Asian (SAS) AF: 0.474 AC: 2287 AN: 4822

European-Finnish (FIN) AF: 0.448 AC: 4729 AN: 10554

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27780 AN: 67990

Other (OTH) AF: 0.332 AC: 699 AN: 2108

Alfa AF: 0.358 Hom.: 2708

Bravo AF: 0.283

Asia WGS AF: 0.395 AC: 1374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.9
DANN	Benign	0.75
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs17706620; hg19: chr7-41918539;