6-164010016-C-T

Variant names:

• chr6-164010016-C-T
• rs206012
• ENST00000850151.1:n.106-47032C>T

Variant summary

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

The ENST00000850151.1(ENSG00000288696):​n.106-47032C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 152,020 control chromosomes in the GnomAD database, including 48,431 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 0.80 (48431 hom., cov: 31)
• Consequence: ENSG00000288696 ENST00000850151.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565
• Publications: 4 publications found

Genes affected

ENSG00000288696 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850151.1. 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
	ENSG00000288696	ENST00000850151.1		n.106-47032C>T		intron	N/A
	ENSG00000288696	ENST00000850152.1		n.166-47032C>T		intron	N/A
	ENSG00000288696	ENST00000850153.1		n.550-47032C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121147 AN: 151902 Hom.: 48368 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.798 AC: 121271 AN: 152020 Hom.: 48431 Cov.: 31 AF XY: 0.801 AC XY: 59540 AN XY: 74318

African (AFR) AF: 0.819 AC: 33970 AN: 41456

American (AMR) AF: 0.819 AC: 12519 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2819 AN: 3472

East Asian (EAS) AF: 0.824 AC: 4247 AN: 5156

South Asian (SAS) AF: 0.837 AC: 4032 AN: 4818

European-Finnish (FIN) AF: 0.823 AC: 8687 AN: 10558

Middle Eastern (MID) AF: 0.798 AC: 233 AN: 292

European-Non Finnish (NFE) AF: 0.770 AC: 52303 AN: 67968

Other (OTH) AF: 0.788 AC: 1659 AN: 2106

Alfa AF: 0.796 Hom.: 8049

Bravo AF: 0.802

Asia WGS AF: 0.849 AC: 2952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.81
DANN	Benign	0.82
PhyloP100		-0.56

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs206012;

hg19: chr6-164431048;