rs9646271

chr16-13953561-C-T

Variant summary

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

The ENST00000576600.1(ENSG00000263234):n.268+139C>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 0.235 in 151,966 control chromosomes in the GnomAD database, including 4,539 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 (4538 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: ENST00000576600.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.337

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 (NFE) allele frequency at 95% confidence interval = 0.278 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
	ENST00000576600.1	n.268+139C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35695 AN: 151842 Hom.: 4534 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.271

GnomAD4 exome AF: 0.500 AC: 3 AN: 6 Hom.: 1 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.235 AC: 35721 AN: 151960 Hom.: 4538 Cov.: 32 AF XY: 0.232 AC XY: 17247 AN XY: 74270

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.273

Alfa AF: 0.276 Hom.: 9194

Bravo AF: 0.229

Asia WGS AF: 0.269 AC: 937 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	2.1
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9646271; hg19: chr16-14047418;