6-129567544-C-T

Variant names:

• chr6-129567544-C-T
• rs9385500
• XR_001743859.2:n.2023G>A

Variant summary

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

The XR_001743859.2(LOC102723409):​n.2023G>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 0.346 in 152,024 control chromosomes in the GnomAD database, including 9,446 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 0.35 (9446 hom., cov: 32)
• Consequence: LOC102723409 XR_001743859.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723409	XR_001743859.2	n.2023G>A		non_coding_transcript_exon_variant	Exon 1 of 7
LOC102723409	XR_001743860.2	n.2023G>A		non_coding_transcript_exon_variant	Exon 1 of 8
LOC102723409	XR_007059754.1	n.2023G>A		non_coding_transcript_exon_variant	Exon 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226149	ENST00000657779.1	n.48+7832G>A		intron_variant	Intron 1 of 9
ENSG00000226149	ENST00000665046.1	n.30+8474G>A		intron_variant	Intron 1 of 9
ENSG00000226149	ENST00000670413.1	n.48+7832G>A		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52631 AN: 151906 Hom.: 9446 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.346 AC: 52642 AN: 152024 Hom.: 9446 Cov.: 32 AF XY: 0.351 AC XY: 26076 AN XY: 74306

African (AFR) AF: 0.284 AC: 11784 AN: 41470

American (AMR) AF: 0.318 AC: 4861 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1181 AN: 3470

East Asian (EAS) AF: 0.482 AC: 2487 AN: 5158

South Asian (SAS) AF: 0.444 AC: 2137 AN: 4818

European-Finnish (FIN) AF: 0.385 AC: 4062 AN: 10554

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24702 AN: 67948

Other (OTH) AF: 0.346 AC: 730 AN: 2110

Alfa AF: 0.362 Hom.: 5895

Bravo AF: 0.339

Asia WGS AF: 0.461 AC: 1604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.55
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs9385500; hg19: chr6-129888689;