rs2151370

Variant names:

• chr9-117962809-A-C
• rs2151370
• ENST00000665764.1:n.*17-9290A>C

Variant summary

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

The ENST00000665764.1(ENSG00000285082):​n.*17-9290A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,106 control chromosomes in the GnomAD database, including 9,306 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 (9306 hom., cov: 33)
• Consequence: ENSG00000285082 ENST00000665764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.630
• Publications: 2 publications found

Genes affected

ENSG00000285082 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665764.1. 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
	ENSG00000285082	ENST00000665764.1		n.*17-9290A>C		intron	N/A	ENSP00000499745.1	A0A2R8YGN2
	ENSG00000285082	ENST00000697636.1		n.*17-94221A>C		intron	N/A	ENSP00000513366.1	A0A2R8YGN2
	ENSG00000284977	ENST00000697639.1		n.1054-94221A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51085 AN: 151988 Hom.: 9301 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.336 AC: 51107 AN: 152106 Hom.: 9306 Cov.: 33 AF XY: 0.344 AC XY: 25576 AN XY: 74348

African (AFR) AF: 0.198 AC: 8225 AN: 41518

American (AMR) AF: 0.328 AC: 5012 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 934 AN: 3472

East Asian (EAS) AF: 0.412 AC: 2133 AN: 5172

South Asian (SAS) AF: 0.457 AC: 2205 AN: 4822

European-Finnish (FIN) AF: 0.537 AC: 5667 AN: 10560

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25817 AN: 67964

Other (OTH) AF: 0.313 AC: 662 AN: 2112

Alfa AF: 0.350 Hom.: 1674

Bravo AF: 0.315

Asia WGS AF: 0.394 AC: 1370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.5
DANN	Benign	0.48
PhyloP100		0.63

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: rs2151370;

hg19: chr9-120725087;