rs9656709

Variant names:

• chr7-55656752-A-C
• rs9656709
• ENST00000825602.1:n.121T>G

Variant summary

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

The ENST00000825602.1(ENSG00000307388):​n.121T>G 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 0.463 in 152,128 control chromosomes in the GnomAD database, including 16,591 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 0.46 (16548 hom., cov: 31)
  • Exomes 𝑓: 0.59 (43 hom.)
• Consequence: ENSG00000307388 ENST00000825602.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 3 publications found

Genes affected

ENSG00000307388 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 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
ENSG00000307388	ENST00000825602.1	n.121T>G		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000231317	ENST00000432235.1	n.*16T>G		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70277 AN: 151780 Hom.: 16549 Cov.: 31

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.512

GnomAD4 exome AF: 0.591 AC: 136 AN: 230 Hom.: 43 Cov.: 0 AF XY: 0.537 AC XY: 72 AN XY: 134

African (AFR) AF: 0.571 AC: 8 AN: 14

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.333 AC: 2 AN: 6

European-Finnish (FIN) AF: 0.143 AC: 2 AN: 14

Middle Eastern (MID) AF: 0.675 AC: 108 AN: 160

European-Non Finnish (NFE) AF: 0.545 AC: 12 AN: 22

Other (OTH) AF: 0.333 AC: 4 AN: 12

GnomAD4 genome AF: 0.463 AC: 70305 AN: 151898 Hom.: 16548 Cov.: 31 AF XY: 0.456 AC XY: 33839 AN XY: 74250

African (AFR) AF: 0.439 AC: 18179 AN: 41410

American (AMR) AF: 0.441 AC: 6723 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2261 AN: 3466

East Asian (EAS) AF: 0.275 AC: 1418 AN: 5160

South Asian (SAS) AF: 0.407 AC: 1956 AN: 4810

European-Finnish (FIN) AF: 0.404 AC: 4263 AN: 10548

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33866 AN: 67944

Other (OTH) AF: 0.510 AC: 1077 AN: 2112

Alfa AF: 0.488 Hom.: 16944

Bravo AF: 0.466

Asia WGS AF: 0.357 AC: 1240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.20
DANN	Benign	0.33
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs9656709; hg19: chr7-55724445;