rs1588368

Variant names:

• chr17-62938848-A-G
• rs1588368
• ENST00000636248.2:n.51-1983T>C

Variant summary

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

The ENST00000636248.2(ENSG00000283538):​n.51-1983T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,130 control chromosomes in the GnomAD database, including 4,796 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 0.22 (4796 hom., cov: 32)
• Consequence: ENSG00000283538 ENST00000636248.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.921
• Publications: 6 publications found

Genes affected

ENSG00000283538 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.302 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
ENSG00000283538	ENST00000636248.2	n.51-1983T>C		intron_variant	Intron 1 of 4	5
ENSG00000283538	ENST00000650312.1	n.128-1983T>C		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33519 AN: 152012 Hom.: 4796 Cov.: 32

Gnomad AFR AF: 0.0576

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.0613

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.220 AC: 33516 AN: 152130 Hom.: 4796 Cov.: 32 AF XY: 0.220 AC XY: 16325 AN XY: 74368

African (AFR) AF: 0.0574 AC: 2386 AN: 41562

American (AMR) AF: 0.272 AC: 4152 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 773 AN: 3464

East Asian (EAS) AF: 0.0613 AC: 318 AN: 5188

South Asian (SAS) AF: 0.160 AC: 770 AN: 4820

European-Finnish (FIN) AF: 0.327 AC: 3451 AN: 10564

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20731 AN: 67930

Other (OTH) AF: 0.217 AC: 459 AN: 2116

Alfa AF: 0.275 Hom.: 10325

Bravo AF: 0.208

Asia WGS AF: 0.124 AC: 432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	12
DANN	Benign	0.76
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs1588368; hg19: chr17-61016209;