rs7799039

Variant names:

• chr7-128238730-G-A
• rs7799039
• ENST00000785131.1:n.169-17190C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-128238730-G-A
• chr7-128238730-G-C

Variant summary

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

The ENST00000785131.1(ENSG00000289434):​n.169-17190C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 152,070 control chromosomes in the GnomAD database, including 12,642 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 0.37 (12642 hom., cov: 33)
• Consequence: ENSG00000289434 ENST00000785131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793
• Publications: 277 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 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.169-17190C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55641 AN: 151952 Hom.: 12638 Cov.: 33

Gnomad AFR AF: 0.0976

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.366 AC: 55647 AN: 152070 Hom.: 12642 Cov.: 33 AF XY: 0.377 AC XY: 28003 AN XY: 74334

African (AFR) AF: 0.0973 AC: 4039 AN: 41502

American (AMR) AF: 0.432 AC: 6593 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1452 AN: 3472

East Asian (EAS) AF: 0.744 AC: 3844 AN: 5168

South Asian (SAS) AF: 0.525 AC: 2525 AN: 4808

European-Finnish (FIN) AF: 0.510 AC: 5389 AN: 10564

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30503 AN: 67972

Other (OTH) AF: 0.370 AC: 780 AN: 2106

Alfa AF: 0.310 Hom.: 4067

Bravo AF: 0.345

Asia WGS AF: 0.621 AC: 2156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.66
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs7799039; hg19: chr7-127878783;