rs9836484

Variant names:

• chr3-77995538-G-A
• rs9836484
• ENST00000756757.1:n.234+27263C>T

Variant summary

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

The ENST00000756757.1(ENSG00000298601):​n.234+27263C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,524 control chromosomes in the GnomAD database, including 8,900 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 0.34 (8900 hom., cov: 31)
• Consequence: ENSG00000298601 ENST00000756757.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782
• Publications: 12 publications found

Genes affected

ENSG00000298601 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756757.1. 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
	ENSG00000298601	ENST00000756757.1		n.234+27263C>T		intron	N/A
	ENSG00000298601	ENST00000756759.1		n.189+27263C>T		intron	N/A
	ENSG00000298601	ENST00000756760.1		n.220+27263C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51194 AN: 151406 Hom.: 8883 Cov.: 31

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.338 AC: 51244 AN: 151524 Hom.: 8900 Cov.: 31 AF XY: 0.334 AC XY: 24743 AN XY: 74034

African (AFR) AF: 0.353 AC: 14594 AN: 41322

American (AMR) AF: 0.243 AC: 3693 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1175 AN: 3460

East Asian (EAS) AF: 0.462 AC: 2363 AN: 5116

South Asian (SAS) AF: 0.231 AC: 1110 AN: 4808

European-Finnish (FIN) AF: 0.341 AC: 3581 AN: 10506

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23606 AN: 67808

Other (OTH) AF: 0.319 AC: 673 AN: 2108

Alfa AF: 0.347 Hom.: 32923

Bravo AF: 0.336

Asia WGS AF: 0.348 AC: 1209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.37
DANN	Benign	0.56
PhyloP100		-0.78

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: rs9836484;

hg19: chr3-78044689;