16-35526596-C-T

Variant names:

• chr16-35526596-C-T
• rs171125
• ENST00000797769.1:n.256+9452C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000797769.1(ENSG00000287448):​n.256+9452C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.085 in 152,238 control chromosomes in the GnomAD database, including 704 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 0.085 (704 hom., cov: 33)
• Consequence: ENSG00000287448 ENST00000797769.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• Publications: 6 publications found

Genes affected

ENSG00000287448 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000797769.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287448	ENST00000797769.1		n.256+9452C>T		intron	N/A
	ENSG00000287448	ENST00000797770.1		n.486+9452C>T		intron	N/A
	ENSG00000287448	ENST00000797771.1		n.347+9452C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0851 AC: 12946 AN: 152120 Hom.: 702 Cov.: 33

Gnomad AFR AF: 0.0186

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0565

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0994

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0987

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

GnomAD4 genome AF: 0.0850 AC: 12946 AN: 152238 Hom.: 704 Cov.: 33 AF XY: 0.0885 AC XY: 6587 AN XY: 74440

African (AFR) AF: 0.0185 AC: 770 AN: 41560

American (AMR) AF: 0.135 AC: 2066 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 661 AN: 3472

East Asian (EAS) AF: 0.0563 AC: 290 AN: 5154

South Asian (SAS) AF: 0.147 AC: 710 AN: 4822

European-Finnish (FIN) AF: 0.0994 AC: 1054 AN: 10608

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7113 AN: 68012

Other (OTH) AF: 0.0976 AC: 206 AN: 2110

Alfa AF: 0.0976 Hom.: 1068

Bravo AF: 0.0822

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	6.2
DANN	Benign	0.84
PhyloP100		0.27

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs171125;

hg19: chr16-34760967;