rs16960244

chr15-47862385-T-C

Variant summary

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

The ENST00000662551.1(ENSG00000259754):n.188+49469T>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 0.104 in 152,274 control chromosomes in the GnomAD database, including 1,431 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 0.10 (1431 hom., cov: 32)
• Consequence: ENST00000662551.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144

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 (AFR) allele frequency at 95% confidence interval = 0.226 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
	ENST00000662551.1	n.188+49469T>C		intron_variant, non_coding_transcript_variant
	ENST00000664705.1	n.188+49469T>C		intron_variant, non_coding_transcript_variant
	ENST00000665188.1	n.68+49469T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15748 AN: 152156 Hom.: 1426 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0566

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.0389

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0401

Gnomad OTH AF: 0.0808

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

GnomAD4 genome AF: 0.104 AC: 15783 AN: 152274 Hom.: 1431 Cov.: 32 AF XY: 0.105 AC XY: 7810 AN XY: 74452

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.0566

Gnomad4 ASJ AF: 0.0784

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.0389

Gnomad4 NFE AF: 0.0400

Gnomad4 OTH AF: 0.0861

Alfa AF: 0.0918 Hom.: 193

Bravo AF: 0.107

Asia WGS AF: 0.203 AC: 703 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	13
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16960244; hg19: chr15-48154582;