rs9646271

Variant names:

• chr16-13953561-C-T
• rs9646271
• ENST00000576600.1:n.268+139C>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 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: ENSG00000263234 ENST00000576600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.337

Genes affected

ENSG00000263234 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000263234	ENST00000576600.1	n.268+139C>T		intron_variant	Intron 1 of 1	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;