rs343496

Variant names:

• chr9-6068077-A-T
• rs343496
• XR_007061410.1:n.139+77T>A

Variant summary

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

The XR_007061410.1(LOC124902116):​n.139+77T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,174 control chromosomes in the GnomAD database, including 2,368 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 0.17 (2368 hom., cov: 32)
• Consequence: LOC124902116 XR_007061410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 10 publications found

Genes affected

LOC124902116 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.21 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: 0.170 AC: 25781 AN: 152056 Hom.: 2362 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.0171

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.170 AC: 25803 AN: 152174 Hom.: 2368 Cov.: 32 AF XY: 0.170 AC XY: 12643 AN XY: 74434

African (AFR) AF: 0.142 AC: 5894 AN: 41500

American (AMR) AF: 0.161 AC: 2457 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 846 AN: 3470

East Asian (EAS) AF: 0.0172 AC: 89 AN: 5188

South Asian (SAS) AF: 0.221 AC: 1066 AN: 4828

European-Finnish (FIN) AF: 0.173 AC: 1839 AN: 10602

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12946 AN: 67974

Other (OTH) AF: 0.202 AC: 427 AN: 2114

Alfa AF: 0.188 Hom.: 396

Bravo AF: 0.163

Asia WGS AF: 0.137 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	12
DANN	Benign	0.83
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs343496; hg19: chr9-6068077; COSMIC: COSV71430052;