7-129791154-G-A

Variant names:

• chr7-129791154-G-A
• rs2693737
• ENST00000807467.1:n.97-1878G>A

Variant summary

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

The ENST00000807467.1(ENSG00000290319):​n.97-1878G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.911 in 152,232 control chromosomes in the GnomAD database, including 63,320 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 0.91 (63320 hom., cov: 31)
• Consequence: ENSG00000290319 ENST00000807467.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 7 publications found

Genes affected

ENSG00000290319 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807467.1. 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
	ENSG00000290319	ENST00000807467.1		n.97-1878G>A		intron	N/A
	ENSG00000290319	ENST00000807468.1		n.290-1878G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.911 AC: 138647 AN: 152114 Hom.: 63267 Cov.: 31

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.975

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.912

Gnomad OTH AF: 0.916

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

GnomAD4 genome AF: 0.911 AC: 138757 AN: 152232 Hom.: 63320 Cov.: 31 AF XY: 0.914 AC XY: 67979 AN XY: 74404

African (AFR) AF: 0.882 AC: 36656 AN: 41544

American (AMR) AF: 0.936 AC: 14324 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.976 AC: 3390 AN: 3472

East Asian (EAS) AF: 0.968 AC: 5002 AN: 5168

South Asian (SAS) AF: 0.976 AC: 4702 AN: 4820

European-Finnish (FIN) AF: 0.906 AC: 9592 AN: 10590

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.912 AC: 62017 AN: 68020

Other (OTH) AF: 0.917 AC: 1937 AN: 2112

Alfa AF: 0.913 Hom.: 142873

Bravo AF: 0.913

Asia WGS AF: 0.971 AC: 3378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.0070
DANN	Benign	0.64
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2693737; hg19: chr7-129430994;