rs846950

Variant names:

• chr6-107697917-C-T
• rs846950
• ENST00000623300.1:n.2302G>A

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000280135 ENST00000623300.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132
• Publications: 4 publications found

Genes affected

ENSG00000280135 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000623300.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000280135	ENST00000623300.1	TSL:6	n.2302G>A		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.625 AC: 5 AN: 8

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.571 AC: 8 AN: 14

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.737 AC: 30549 AN: 41468

American (AMR) AF: 0.617 AC: 9416 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2423 AN: 3470

East Asian (EAS) AF: 0.401 AC: 2073 AN: 5172

South Asian (SAS) AF: 0.621 AC: 2990 AN: 4816

European-Finnish (FIN) AF: 0.541 AC: 5700 AN: 10528

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43261 AN: 67978

Other (OTH) AF: 0.644 AC: 1361 AN: 2114

Alfa AF: 0.638 Hom.: 130480

Bravo AF: 0.653

Asia WGS AF: 0.536 AC: 1864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.3
DANN	Benign	0.45
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs846950; hg19: chr6-108019121;