chr7-129765967-A-G

Position:

• chr7-129765967-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000660838.1(ENSG00000286380):​n.587+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 ENST00000660838.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440

Genes affected

ENSG00000286380 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375501	XR_927963.4	n.590+1920T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286380	ENST00000660838.1	n.587+1920T>C		intron_variant
ENSG00000286380	ENST00000704489.2	n.1042-1045T>C		intron_variant
ENSG00000286380	ENST00000704490.1	n.368+1920T>C		intron_variant
ENSG00000286380	ENST00000710872.1	n.432-2561T>C		intron_variant

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

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.250

Alfa AF: 0.251 Hom.: 4906

Bravo AF: 0.251

Asia WGS AF: 0.234 AC: 811 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	0.76
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2402959; hg19: chr7-129405807;