rs791600

chr7-128225763-G-A

Variant summary

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

The ENST00000692614.2(ENSG00000289434):n.520-4223C>T 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 0.404 in 151,962 control chromosomes in the GnomAD database, including 12,768 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 0.40 (12768 hom., cov: 32)
• Consequence: ENST00000692614.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.565

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.685 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
	ENST00000692614.2	n.520-4223C>T		intron_variant, non_coding_transcript_variant
	ENST00000690022.1	n.244-4223C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61294 AN: 151842 Hom.: 12763 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.426

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.404 AC: 61325 AN: 151962 Hom.: 12768 Cov.: 32 AF XY: 0.405 AC XY: 30063 AN XY: 74268

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.429

Alfa AF: 0.409 Hom.: 19479

Bravo AF: 0.397

Asia WGS AF: 0.536 AC: 1860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	6.0
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs791600; hg19: chr7-127865816;