rs2157673

Variant names:

• chr9-115796830-T-C
• rs2157673
• ENST00000832032.1:n.321+47501A>G

Variant summary

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

The ENST00000832032.1(ENSG00000228714):​n.321+47501A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,870 control chromosomes in the GnomAD database, including 7,529 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 0.31 (7529 hom., cov: 32)
• Consequence: ENSG00000228714 ENST00000832032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304
• Publications: 3 publications found

Genes affected

ENSG00000228714 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832032.1. 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
	ENSG00000228714	ENST00000832032.1		n.321+47501A>G		intron	N/A
	ENSG00000308189	ENST00000832372.1		n.305+49104T>C		intron	N/A
	ENSG00000308189	ENST00000832373.1		n.335-29755T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47506 AN: 151750 Hom.: 7516 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.313 AC: 47547 AN: 151870 Hom.: 7529 Cov.: 32 AF XY: 0.315 AC XY: 23408 AN XY: 74242

African (AFR) AF: 0.280 AC: 11601 AN: 41382

American (AMR) AF: 0.341 AC: 5212 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1246 AN: 3466

East Asian (EAS) AF: 0.409 AC: 2110 AN: 5154

South Asian (SAS) AF: 0.295 AC: 1422 AN: 4826

European-Finnish (FIN) AF: 0.320 AC: 3365 AN: 10528

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.318 AC: 21612 AN: 67932

Other (OTH) AF: 0.321 AC: 676 AN: 2108

Alfa AF: 0.320 Hom.: 29077

Bravo AF: 0.315

Asia WGS AF: 0.346 AC: 1201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.68
PhyloP100		0.30

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: rs2157673;

hg19: chr9-118559109;