rs6466115

Variant names:

• chr7-106471226-A-G
• rs6466115
• ENST00000475791.5:n.253-5290T>C

Variant summary

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

The ENST00000475791.5(ENSG00000243797):​n.253-5290T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 151,996 control chromosomes in the GnomAD database, including 8,749 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 0.25 (8749 hom., cov: 32)
• Consequence: ENSG00000243797 ENST00000475791.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 3 publications found

Genes affected

ENSG00000243797 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000243797	ENST00000475791.5	n.253-5290T>C		intron_variant	Intron 2 of 3	3
ENSG00000243797	ENST00000490856.5	n.387+19784T>C		intron_variant	Intron 4 of 4	4
ENSG00000286076	ENST00000651902.1	n.220-40000A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38125 AN: 151878 Hom.: 8732 Cov.: 32

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.0753

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.251 AC: 38199 AN: 151996 Hom.: 8749 Cov.: 32 AF XY: 0.246 AC XY: 18270 AN XY: 74310

African (AFR) AF: 0.616 AC: 25487 AN: 41404

American (AMR) AF: 0.133 AC: 2037 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0753 AC: 261 AN: 3468

East Asian (EAS) AF: 0.164 AC: 849 AN: 5174

South Asian (SAS) AF: 0.145 AC: 700 AN: 4818

European-Finnish (FIN) AF: 0.102 AC: 1085 AN: 10592

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7168 AN: 67966

Other (OTH) AF: 0.214 AC: 451 AN: 2106

Alfa AF: 0.231 Hom.: 1346

Bravo AF: 0.267

Asia WGS AF: 0.193 AC: 672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.40
DANN	Benign	0.67
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs6466115; hg19: chr7-106111672;