7-129765967-A-G

Variant names:

• chr7-129765967-A-G
• rs2402959
• ENST00000660838.2:n.591+1920T>C

Variant summary

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

The ENST00000660838.2(ENSG00000286380):​n.591+1920T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,126 control chromosomes in the GnomAD database, including 5,079 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 0.26 (5079 hom., cov: 32)
• Consequence: ENSG00000286380 ENST00000660838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440
• Publications: 12 publications found

Genes affected

ENSG00000286380 (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 (EAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660838.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286380	ENST00000660838.2		n.591+1920T>C		intron	N/A
	ENSG00000286380	ENST00000704489.2		n.1042-1045T>C		intron	N/A
	ENSG00000286380	ENST00000704490.1		n.368+1920T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38984 AN: 152008 Hom.: 5079 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.256 AC: 38995 AN: 152126 Hom.: 5079 Cov.: 32 AF XY: 0.258 AC XY: 19204 AN XY: 74362

African (AFR) AF: 0.246 AC: 10207 AN: 41474

American (AMR) AF: 0.243 AC: 3714 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 674 AN: 3472

East Asian (EAS) AF: 0.319 AC: 1651 AN: 5172

South Asian (SAS) AF: 0.225 AC: 1088 AN: 4826

European-Finnish (FIN) AF: 0.302 AC: 3193 AN: 10580

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17708 AN: 67990

Other (OTH) AF: 0.250 AC: 530 AN: 2116

Alfa AF: 0.252 Hom.: 6529

Bravo AF: 0.251

Asia WGS AF: 0.234 AC: 811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.76
DANN	Benign	0.71
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs2402959; hg19: chr7-129405807;