chr7-25483647-G-A

Variant names:

• chr7-25483647-G-A
• rs7791702
• ENST00000650415.1:n.199+1731G>A

Variant summary

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

The ENST00000650415.1(ENSG00000285960):​n.199+1731G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,046 control chromosomes in the GnomAD database, including 9,542 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 0.35 (9542 hom., cov: 32)
• Consequence: ENSG00000285960 ENST00000650415.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220

Genes affected

ENSG00000285960 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 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
ENSG00000285960	ENST00000650415.1	n.199+1731G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53372 AN: 151928 Hom.: 9531 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.351 AC: 53410 AN: 152046 Hom.: 9542 Cov.: 32 AF XY: 0.348 AC XY: 25830 AN XY: 74316

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.356

Alfa AF: 0.359 Hom.: 3114

Bravo AF: 0.347

Asia WGS AF: 0.306 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7791702; hg19: chr7-25523266;