3-115514065-T-C

Variant summary

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

The ENST00000662602.1(ENSG00000242880):n.818-50121T>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 0.484 in 152,044 control chromosomes in the GnomAD database, including 18,115 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 0.48 (18115 hom., cov: 33)
• Consequence: ENST00000662602.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.568 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
	ENST00000662602.1	n.818-50121T>C		intron_variant, non_coding_transcript_variant
	ENST00000657371.1	n.593-50121T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73505 AN: 151924 Hom.: 18086 Cov.: 33

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.484 AC: 73572 AN: 152044 Hom.: 18115 Cov.: 33 AF XY: 0.489 AC XY: 36361 AN XY: 74322

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.499

Alfa AF: 0.503 Hom.: 38535

Bravo AF: 0.480

Asia WGS AF: 0.576 AC: 1998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	12
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: rs10511343; hg19: chr3-115232912;