rs1588368

Positions:

• chr17-62938848-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000636248.2(ENSG00000283538):​n.51-1983T>C variant causes a intron, non coding transcript 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: ENST00000636248.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.921

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000636248.2	n.51-1983T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000650312.1	n.128-1983T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0574

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.0613

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.217

Alfa AF: 0.281 Hom.: 8467

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1588368; hg19: chr17-61016209;