rs9321172

Variant names:

• chr6-129556854-C-T
• rs9321172
• XR_007059755.1:n.1197G>A

Variant summary

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

The XR_007059755.1(LOC102723409):​n.1197G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,102 control chromosomes in the GnomAD database, including 5,161 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 0.24 (5161 hom., cov: 33)
• Consequence: LOC102723409 XR_007059755.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 6 publications found

Genes affected

LOC102723409 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723409	XR_007059755.1	n.1197G>A		non_coding_transcript_exon_variant	Exon 1 of 10
LOC102723409	XR_007059756.1	n.1197G>A		non_coding_transcript_exon_variant	Exon 1 of 11
LOC102723409	XR_007059757.1	n.1197G>A		non_coding_transcript_exon_variant	Exon 1 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226149	ENST00000657779.1	n.157+1204G>A		intron_variant	Intron 2 of 9
ENSG00000226149	ENST00000665046.1	n.139+1204G>A		intron_variant	Intron 2 of 9
ENSG00000226149	ENST00000670413.1	n.157+1204G>A		intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36322 AN: 151984 Hom.: 5162 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.0948

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.239 AC: 36325 AN: 152102 Hom.: 5161 Cov.: 33 AF XY: 0.232 AC XY: 17262 AN XY: 74338

African (AFR) AF: 0.101 AC: 4178 AN: 41512

American (AMR) AF: 0.222 AC: 3387 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1166 AN: 3472

East Asian (EAS) AF: 0.0950 AC: 491 AN: 5170

South Asian (SAS) AF: 0.180 AC: 870 AN: 4828

European-Finnish (FIN) AF: 0.285 AC: 3020 AN: 10580

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22354 AN: 67948

Other (OTH) AF: 0.266 AC: 561 AN: 2106

Alfa AF: 0.302 Hom.: 14146

Bravo AF: 0.229

Asia WGS AF: 0.144 AC: 502 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.11
DANN	Benign	0.52
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs9321172; hg19: chr6-129877999;