rs7694379

chr4-87265357-G-Achr4-87265357-G-C

Variant summary

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

The ENST00000503666.1(ENSG00000250572):n.88+1378C>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 0.397 in 152,030 control chromosomes in the GnomAD database, including 12,180 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 (12180 hom., cov: 32)
• Consequence: ENST00000503666.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.777

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.427 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
	ENST00000503666.1	n.88+1378C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60396 AN: 151912 Hom.: 12174 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.397 AC: 60425 AN: 152030 Hom.: 12180 Cov.: 32 AF XY: 0.388 AC XY: 28795 AN XY: 74302

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.385

Alfa AF: 0.400 Hom.: 5914

Bravo AF: 0.404

Asia WGS AF: 0.299 AC: 1041 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.5
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7694379; hg19: chr4-88186509;