6-31297713-T-C

Position:

• chr6-31297713-T-C

Variant summary

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

The XR_926691.3(LOC112267902):​n.1924A>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 0.804 in 152,104 control chromosomes in the GnomAD database, including 49,582 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 0.80 (49582 hom., cov: 31)
• Consequence: LOC112267902 XR_926691.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361

Genes affected

LOC112267902 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC112267902	XR_926691.3	n.1924A>G		non_coding_transcript_exon_variant	5/5
LINC02571	NR_149115.1	n.167-2700A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02571	ENST00000539514.1	n.172-2700A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122155 AN: 151986 Hom.: 49526 Cov.: 31

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.804 AC: 122262 AN: 152104 Hom.: 49582 Cov.: 31 AF XY: 0.809 AC XY: 60136 AN XY: 74340

Gnomad4 AFR AF: 0.876

Gnomad4 AMR AF: 0.848

Gnomad4 ASJ AF: 0.930

Gnomad4 EAS AF: 0.839

Gnomad4 SAS AF: 0.881

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.739

Gnomad4 OTH AF: 0.855

Alfa AF: 0.764 Hom.: 81355

Bravo AF: 0.813

Asia WGS AF: 0.883 AC: 3072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.9
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2247056; hg19: chr6-31265490;