rs846951

Variant names:

• chr6-107697078-G-A
• rs846951
• ENST00000623300.1:n.*221C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000623300.1(ENSG00000280135):​n.*221C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 152,040 control chromosomes in the GnomAD database, including 35,607 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 0.68 (35607 hom., cov: 31)
• Consequence: ENSG00000280135 ENST00000623300.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 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.*221C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103478 AN: 151922 Hom.: 35573 Cov.: 31

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.681 AC: 103568 AN: 152040 Hom.: 35607 Cov.: 31 AF XY: 0.676 AC XY: 50220 AN XY: 74296

African (AFR) AF: 0.777 AC: 32216 AN: 41472

American (AMR) AF: 0.631 AC: 9633 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2430 AN: 3472

East Asian (EAS) AF: 0.570 AC: 2944 AN: 5164

South Asian (SAS) AF: 0.631 AC: 3038 AN: 4814

European-Finnish (FIN) AF: 0.577 AC: 6084 AN: 10550

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 45024 AN: 67976

Other (OTH) AF: 0.664 AC: 1403 AN: 2112

Alfa AF: 0.687 Hom.: 7053

Bravo AF: 0.685

Asia WGS AF: 0.618 AC: 2152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.56
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs846951; hg19: chr6-108018282;