rs7791702

chr7-25483647-G-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, non coding transcript 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: ENST00000650415.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650415.1	n.199+1731G>A		intron_variant, non_coding_transcript_variant

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;