rs13214956

chr6-129567889-C-T

Variant summary

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

The XR_001743860.2(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_001743860.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640

Genes affected

LOC102723409 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC102723409	XR_001743860.2	n.1678G>A		non_coding_transcript_exon_variant	1/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000665046.1	n.30+8129G>A		intron_variant, non_coding_transcript_variant
	ENST00000657779.1	n.48+7487G>A		intron_variant, non_coding_transcript_variant
	ENST00000670413.1	n.48+7487G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.00991

Gnomad4 AMR AF: 0.0638

Gnomad4 ASJ AF: 0.0118

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.0390

Gnomad4 FIN AF: 0.0723

Gnomad4 NFE AF: 0.0487

Gnomad4 OTH AF: 0.0511

Alfa AF: 0.0474 Hom.: 165

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13214956; hg19: chr6-129889034;