rs7620754

chr3-114229128-T-C

Variant summary

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

The ENST00000493033.1(ENSG00000241490):n.161-4214T>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 0.243 in 151,846 control chromosomes in the GnomAD database, including 4,635 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 0.24 (4635 hom., cov: 31)
• Consequence: ENST00000493033.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 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
	ENST00000493033.1	n.161-4214T>C		intron_variant, non_coding_transcript_variant		2
	ENST00000481773.1	n.239-4214T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36817 AN: 151728 Hom.: 4630 Cov.: 31

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.243 AC: 36834 AN: 151846 Hom.: 4635 Cov.: 31 AF XY: 0.247 AC XY: 18364 AN XY: 74234

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.260

Alfa AF: 0.236 Hom.: 5475

Bravo AF: 0.243

Asia WGS AF: 0.303 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.8
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7620754; hg19: chr3-113947975;