16-13953561-C-T

Variant names:

• chr16-13953561-C-T
• rs9646271
• ENST00000576600.1:n.268+139C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

ENSG00000263234 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000576600.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000263234	ENST00000576600.1	TSL:4	n.268+139C>T		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 3 AN: 6

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.167 AC: 6905 AN: 41414

American (AMR) AF: 0.187 AC: 2853 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1025 AN: 3468

East Asian (EAS) AF: 0.236 AC: 1220 AN: 5178

South Asian (SAS) AF: 0.243 AC: 1172 AN: 4814

European-Finnish (FIN) AF: 0.235 AC: 2481 AN: 10548

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19122 AN: 67960

Other (OTH) AF: 0.273 AC: 576 AN: 2108

Alfa AF: 0.265 Hom.: 14360

Bravo AF: 0.229

Asia WGS AF: 0.269 AC: 937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.56
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs9646271; hg19: chr16-14047418;