chr6-129566154-T-C

Position:

• chr6-129566154-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001743859.2(LOC102723409):​n.3413A>G 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 0.0994 in 152,268 control chromosomes in the GnomAD database, including 1,000 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 0.099 (1000 hom., cov: 32)
• Consequence: LOC102723409 XR_001743859.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

Genes affected

LOC102723409 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102723409	XR_001743859.2	n.3413A>G		non_coding_transcript_exon_variant	1/7
LOC102723409	XR_001743860.2	n.3413A>G		non_coding_transcript_exon_variant	1/8
LOC102723409	XR_007059754.1	n.3413A>G		non_coding_transcript_exon_variant	1/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000226149	ENST00000657779.1	n.49-7988A>G		intron_variant
ENSG00000226149	ENST00000665046.1	n.31-7988A>G		intron_variant
ENSG00000226149	ENST00000670413.1	n.49-7988A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0995 AC: 15137 AN: 152150 Hom.: 1002 Cov.: 32

Gnomad AFR AF: 0.0250

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0601

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.0994 AC: 15137 AN: 152268 Hom.: 1000 Cov.: 32 AF XY: 0.0972 AC XY: 7233 AN XY: 74434

Gnomad4 AFR AF: 0.0249

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0616

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.120

Alfa AF: 0.130 Hom.: 791

Bravo AF: 0.0974

Asia WGS AF: 0.0290 AC: 100 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.23
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17810534; hg19: chr6-129887299;