7-128259076-A-G

Variant names:

• chr7-128259076-A-G
• rs2060715
• ENST00000785131.1:n.168+4286T>C

Variant summary

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

The ENST00000785131.1(ENSG00000289434):​n.168+4286T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 151,272 control chromosomes in the GnomAD database, including 17,053 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 0.44 (17053 hom., cov: 31)
• Consequence: ENSG00000289434 ENST00000785131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.729
• Publications: 17 publications found

Genes affected

ENSG00000289434 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 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
ENSG00000289434	ENST00000785131.1	n.168+4286T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.442 AC: 66791 AN: 151172 Hom.: 17047 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.442 AC: 66804 AN: 151272 Hom.: 17053 Cov.: 31 AF XY: 0.444 AC XY: 32822 AN XY: 73856

African (AFR) AF: 0.175 AC: 7251 AN: 41422

American (AMR) AF: 0.515 AC: 7814 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1904 AN: 3462

East Asian (EAS) AF: 0.728 AC: 3743 AN: 5144

South Asian (SAS) AF: 0.552 AC: 2645 AN: 4792

European-Finnish (FIN) AF: 0.488 AC: 4993 AN: 10226

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.542 AC: 36756 AN: 67770

Other (OTH) AF: 0.485 AC: 1015 AN: 2094

Alfa AF: 0.520 Hom.: 70788

Bravo AF: 0.429

Asia WGS AF: 0.634 AC: 2202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.29
DANN	Benign	0.73
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs2060715; hg19: chr7-127899129;