XR_001743859.2:n.1678G>A

Variant names:

• chr6-129567889-C-T
• rs13214956
• XR_001743859.2:n.1678G>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.1678G>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 0.0455 in 152,268 control chromosomes in the GnomAD database, including 252 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 0.045 (252 hom., cov: 32)
• Consequence: LOC102723409 XR_001743859.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723409	XR_001743859.2	n.1678G>A		non_coding_transcript_exon_variant	Exon 1 of 7
LOC102723409	XR_001743860.2	n.1678G>A		non_coding_transcript_exon_variant	Exon 1 of 8
LOC102723409	XR_007059754.1	n.1678G>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+7487G>A		intron_variant	Intron 1 of 9
ENSG00000226149	ENST00000665046.1	n.30+8129G>A		intron_variant	Intron 1 of 9
ENSG00000226149	ENST00000670413.1	n.48+7487G>A		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.0455 AC: 6926 AN: 152150 Hom.: 253 Cov.: 32

Gnomad AFR AF: 0.00994

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0639

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.0394

Gnomad FIN AF: 0.0723

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0487

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0455 AC: 6927 AN: 152268 Hom.: 252 Cov.: 32 AF XY: 0.0472 AC XY: 3515 AN XY: 74454

African (AFR) AF: 0.00991 AC: 412 AN: 41558

American (AMR) AF: 0.0638 AC: 976 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3472

East Asian (EAS) AF: 0.198 AC: 1025 AN: 5172

South Asian (SAS) AF: 0.0390 AC: 188 AN: 4824

European-Finnish (FIN) AF: 0.0723 AC: 768 AN: 10616

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0487 AC: 3315 AN: 68018

Other (OTH) AF: 0.0511 AC: 108 AN: 2114

Alfa AF: 0.0467 Hom.: 197

Bravo AF: 0.0450

Asia WGS AF: 0.143 AC: 496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.32
DANN	Benign	0.59
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs13214956; hg19: chr6-129889034;