rs931734

chr4-52430144-G-A

Variant summary

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

The ENST00000660768.1(ENSG00000287999):n.203+79866C>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 0.402 in 151,958 control chromosomes in the GnomAD database, including 13,752 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 (13752 hom., cov: 31)
• Consequence: ENST00000660768.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.51 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
	ENST00000660768.1	n.203+79866C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61042 AN: 151840 Hom.: 13758 Cov.: 31

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.0572

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.402 AC: 61036 AN: 151958 Hom.: 13752 Cov.: 31 AF XY: 0.398 AC XY: 29522 AN XY: 74264

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.0574

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.427

Alfa AF: 0.485 Hom.: 17759

Bravo AF: 0.383

Asia WGS AF: 0.230 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.92
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs931734; hg19: chr4-53296310;