9-118936436-T-C

Variant names:

• chr9-118936436-T-C
• rs12237612
• XR_001746918.2:n.629-14670T>C

Variant summary

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

The XR_001746918.2(LOC101928849):​n.629-14670T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,176 control chromosomes in the GnomAD database, including 1,112 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 0.10 (1112 hom., cov: 32)
• Consequence: LOC101928849 XR_001746918.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 3 publications found

Genes affected

LOC101928849 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15627 AN: 152058 Hom.: 1115 Cov.: 32

Gnomad AFR AF: 0.0231

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.103 AC: 15627 AN: 152176 Hom.: 1112 Cov.: 32 AF XY: 0.106 AC XY: 7872 AN XY: 74388

African (AFR) AF: 0.0230 AC: 956 AN: 41554

American (AMR) AF: 0.109 AC: 1663 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 716 AN: 3468

East Asian (EAS) AF: 0.313 AC: 1613 AN: 5146

South Asian (SAS) AF: 0.209 AC: 1003 AN: 4810

European-Finnish (FIN) AF: 0.113 AC: 1191 AN: 10586

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.120 AC: 8181 AN: 68000

Other (OTH) AF: 0.120 AC: 253 AN: 2116

Alfa AF: 0.118 Hom.: 2226

Bravo AF: 0.0975

Asia WGS AF: 0.208 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.5
DANN	Benign	0.76
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs12237612; hg19: chr9-121698714;