9-104932241-C-T

Variant names:

• chr9-104932241-C-T
• rs2487042
• ENST00000820514.1:n.1164+4331C>T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NR_188620.1(LOC105376196):​n.1339+2517C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,084 control chromosomes in the GnomAD database, including 3,266 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.19 (3266 hom., cov: 31)
• Consequence: LOC105376196 NR_188620.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36
• Publications: 6 publications found

Genes affected

ENSG00000226334 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_188620.1. 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
	LOC105376196	NR_188620.1		n.1339+2517C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226334	ENST00000820514.1		n.1164+4331C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28571 AN: 151966 Hom.: 3272 Cov.: 31

Gnomad AFR AF: 0.0611

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.188 AC: 28571 AN: 152084 Hom.: 3266 Cov.: 31 AF XY: 0.193 AC XY: 14365 AN XY: 74340

African (AFR) AF: 0.0610 AC: 2532 AN: 41512

American (AMR) AF: 0.190 AC: 2909 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1046 AN: 3470

East Asian (EAS) AF: 0.299 AC: 1543 AN: 5154

South Asian (SAS) AF: 0.356 AC: 1717 AN: 4820

European-Finnish (FIN) AF: 0.285 AC: 3006 AN: 10562

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15183 AN: 67968

Other (OTH) AF: 0.190 AC: 401 AN: 2114

Alfa AF: 0.198 Hom.: 436

Bravo AF: 0.175

Asia WGS AF: 0.300 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Uncertain	-0.060
CADD	Benign	18
DANN	Benign	0.75
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs2487042; hg19: chr9-107694522;