rs554241

chr8-8738102-C-T

Variant summary

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

The ENST00000522213.5(ENSG00000254367):n.625-14368G>A 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 0.165 in 152,030 control chromosomes in the GnomAD database, including 2,562 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 (2562 hom., cov: 32)
• Consequence: ENST00000522213.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 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
	ENST00000522213.5	n.625-14368G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25096 AN: 151914 Hom.: 2557 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.165 AC: 25113 AN: 152030 Hom.: 2562 Cov.: 32 AF XY: 0.163 AC XY: 12133 AN XY: 74308

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.160

Alfa AF: 0.121 Hom.: 654

Bravo AF: 0.169

Asia WGS AF: 0.128 AC: 445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.43
Dann	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs554241; hg19: chr8-8595612;