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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378102	XR_943213.4	n.559-47032C>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288696	ENST00000850151.1	n.106-47032C>T		intron_variant	Intron 1 of 4
ENSG00000288696	ENST00000850152.1	n.166-47032C>T		intron_variant	Intron 1 of 3
ENSG00000288696	ENST00000850153.1	n.550-47032C>T		intron_variant	Intron 3 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs206012; hg19: chr6-164431048;