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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902116	XR_007061410.1	n.139+77T>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;