rs2395163

Variant names:

• chr6-32420032-T-C
• rs2395163
• ENST00000766247.1:n.282+5662T>C

Variant summary

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

The ENST00000766247.1(ENSG00000299769):​n.282+5662T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 151,950 control chromosomes in the GnomAD database, including 2,484 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 0.17 (2484 hom., cov: 31)
• Consequence: ENSG00000299769 ENST00000766247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 84 publications found

Genes affected

ENSG00000299769 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.202 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
ENSG00000299769	ENST00000766247.1	n.282+5662T>C		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766248.1	n.287-5336T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26322 AN: 151830 Hom.: 2487 Cov.: 31

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.173 AC: 26318 AN: 151950 Hom.: 2484 Cov.: 31 AF XY: 0.173 AC XY: 12833 AN XY: 74278

African (AFR) AF: 0.106 AC: 4401 AN: 41440

American (AMR) AF: 0.205 AC: 3134 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 860 AN: 3460

East Asian (EAS) AF: 0.107 AC: 552 AN: 5162

South Asian (SAS) AF: 0.208 AC: 1000 AN: 4814

European-Finnish (FIN) AF: 0.175 AC: 1844 AN: 10534

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13939 AN: 67962

Other (OTH) AF: 0.163 AC: 343 AN: 2108

Alfa AF: 0.202 Hom.: 12107

Bravo AF: 0.178

Asia WGS AF: 0.133 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.57
DANN	Benign	0.33
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2395163; hg19: chr6-32387809;