rs3950186

Positions:

• chr6-11811081-C-T

Variant summary

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

The ENST00000412132.1(ENSG00000234427):​n.387C>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 0.508 in 152,144 control chromosomes in the GnomAD database, including 22,539 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 0.51 (22537 hom., cov: 32)
  • Exomes 𝑓: 0.37 (2 hom.)
• Consequence: ENST00000412132.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986567	XR_001743970.2	n.186G>A		non_coding_transcript_exon_variant	1/3
LOC124901257	XR_007059451.1			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000412132.1	n.387C>T		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes AF: 0.507 AC: 77098 AN: 151980 Hom.: 22488 Cov.: 32

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.478

GnomAD4 exome AF: 0.370 AC: 17 AN: 46 Hom.: 2 Cov.: 0 AF XY: 0.467 AC XY: 14 AN XY: 30

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.281

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.508 AC: 77204 AN: 152098 Hom.: 22537 Cov.: 32 AF XY: 0.513 AC XY: 38135 AN XY: 74346

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.482

Alfa AF: 0.386 Hom.: 5798

Bravo AF: 0.521

Asia WGS AF: 0.553 AC: 1927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3950186; hg19: chr6-11811314;