rs10517255

Positions:

• chr4-32638404-C-A
• chr4-32638404-C-G

Variant summary

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

The ENST00000659320.1(ENSG00000286784):​n.216-53108G>T 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 0.104 in 152,074 control chromosomes in the GnomAD database, including 2,041 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 0.10 (2041 hom., cov: 32)
• Consequence: ENST00000659320.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470

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 (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659320.1	n.216-53108G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15804 AN: 151956 Hom.: 2039 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0718

Gnomad ASJ AF: 0.00433

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.0430

Gnomad FIN AF: 0.0284

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00868

Gnomad OTH AF: 0.0759

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

GnomAD4 genome AF: 0.104 AC: 15831 AN: 152074 Hom.: 2041 Cov.: 32 AF XY: 0.103 AC XY: 7650 AN XY: 74372

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.0719

Gnomad4 ASJ AF: 0.00433

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.0424

Gnomad4 FIN AF: 0.0284

Gnomad4 NFE AF: 0.00868

Gnomad4 OTH AF: 0.0751

Alfa AF: 0.0236 Hom.: 103

Bravo AF: 0.118

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.84
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517255; hg19: chr4-32640026;