rs10503991

Positions:

• chr8-36562484-A-G
• chr8-36562484-A-T

Variant summary

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

The ENST00000656455.1(ENSG00000253363):​n.485-135420T>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 0.203 in 152,102 control chromosomes in the GnomAD database, including 4,596 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 0.20 (4596 hom., cov: 32)
• Consequence: ENST00000656455.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 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
	ENST00000656455.1	n.485-135420T>C		intron_variant, non_coding_transcript_variant
	ENST00000524132.6	n.530-25008T>C		intron_variant, non_coding_transcript_variant		4
	ENST00000651399.1	n.517-66772T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30745 AN: 151984 Hom.: 4579 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.203 AC: 30808 AN: 152102 Hom.: 4596 Cov.: 32 AF XY: 0.204 AC XY: 15137 AN XY: 74358

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.195

Alfa AF: 0.108 Hom.: 604

Bravo AF: 0.211

Asia WGS AF: 0.305 AC: 1057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.6
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503991; hg19: chr8-36420002;