rs3905495

Positions:

• chr6-31297762-G-A
• chr6-31297762-G-T

Variant summary

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

The XR_926691.3(LOC112267902):​n.1875C>T 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 0.394 in 151,982 control chromosomes in the GnomAD database, including 12,060 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 0.39 (12060 hom., cov: 32)
• Consequence: LOC112267902 XR_926691.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

Genes affected

LOC112267902 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC112267902	XR_926691.3	n.1875C>T		non_coding_transcript_exon_variant	5/5
LINC02571	NR_149115.1	n.167-2749C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02571	ENST00000539514.1	n.172-2749C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59817 AN: 151862 Hom.: 12044 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.394 AC: 59866 AN: 151982 Hom.: 12060 Cov.: 32 AF XY: 0.401 AC XY: 29775 AN XY: 74270

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.393

Alfa AF: 0.351 Hom.: 14015

Bravo AF: 0.393

Asia WGS AF: 0.485 AC: 1687 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	6.4
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3905495; hg19: chr6-31265539;