rs11781985

Positions:

• chr8-8732273-T-C

Variant summary

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

The ENST00000522213.5(ENSG00000254367):​n.625-8539A>G 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 0.197 in 152,114 control chromosomes in the GnomAD database, including 3,193 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 (3193 hom., cov: 31)
• Consequence: ENST00000522213.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.222 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
	ENST00000522213.5	n.625-8539A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29969 AN: 151996 Hom.: 3191 Cov.: 31

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0481

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.197 AC: 30001 AN: 152114 Hom.: 3193 Cov.: 31 AF XY: 0.194 AC XY: 14449 AN XY: 74368

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.0480

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.195

Alfa AF: 0.211 Hom.: 3318

Bravo AF: 0.189

Asia WGS AF: 0.104 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11781985; hg19: chr8-8589783;