rs3873386

chr6-31305968-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.964+810A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,932 control chromosomes in the GnomAD database, including 15,675 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 0.45 (15675 hom., cov: 31)
• Consequence: LOC112267902 XR_926691.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.94

Genes affected

LOC112267902 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112267902	XR_926691.3	n.964+810A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67998 AN: 151814 Hom.: 15649 Cov.: 31

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.448 AC: 68064 AN: 151932 Hom.: 15675 Cov.: 31 AF XY: 0.455 AC XY: 33756 AN XY: 74268

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.447

Alfa AF: 0.395 Hom.: 22651

Bravo AF: 0.449

Asia WGS AF: 0.422 AC: 1468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.16
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3873386; hg19: chr6-31273745;