rs1476697

chr7-25436697-T-C

Variant summary

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

The ENST00000650415.1(ENSG00000285960):n.66+4652T>C 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 0.312 in 152,166 control chromosomes in the GnomAD database, including 8,683 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 0.31 (8683 hom., cov: 33)
• Consequence: ENST00000650415.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 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.66+4652T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47432 AN: 152048 Hom.: 8697 Cov.: 33

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.312 AC: 47429 AN: 152166 Hom.: 8683 Cov.: 33 AF XY: 0.319 AC XY: 23764 AN XY: 74392

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.812

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.344

Alfa AF: 0.339 Hom.: 18529

Bravo AF: 0.313

Asia WGS AF: 0.589 AC: 2043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	1.9
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1476697; hg19: chr7-25476316;