rs846950

Positions:

• chr6-107697917-C-T

Variant summary

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

The ENST00000623300.1(ENSG00000280135):​n.2302G>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 0.648 in 152,040 control chromosomes in the GnomAD database, including 32,369 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 0.65 (32366 hom., cov: 32)
  • Exomes 𝑓: 0.58 (3 hom.)
• Consequence: ENST00000623300.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000623300.1	n.2302G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98482 AN: 151898 Hom.: 32332 Cov.: 32

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.643

GnomAD4 exome AF: 0.583 AC: 14 AN: 24 Hom.: 3 Cov.: 0 AF XY: 0.667 AC XY: 8 AN XY: 12

Gnomad4 AFR exome AF: 0.625

Gnomad4 NFE exome AF: 0.571

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.648 AC: 98567 AN: 152016 Hom.: 32366 Cov.: 32 AF XY: 0.644 AC XY: 47834 AN XY: 74282

Gnomad4 AFR AF: 0.737

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.644

Alfa AF: 0.636 Hom.: 62567

Bravo AF: 0.653

Asia WGS AF: 0.536 AC: 1864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.3
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs846950; hg19: chr6-108019121;