rs11781985

Variant names:

• chr8-8732273-T-C
• rs11781985
• ENST00000522213.5:n.625-8539A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000522213.5(ENSG00000254367):​n.625-8539A>G variant causes a intron 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: ENSG00000254367 ENST00000522213.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527
• Publications: 7 publications found

Genes affected

ENSG00000254367 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522213.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254367	ENST00000522213.5	TSL:2	n.625-8539A>G		intron	N/A
	ENSG00000254367	ENST00000765578.1		n.456-8539A>G		intron	N/A
	ENSG00000254367	ENST00000765579.1		n.407-7234A>G		intron	N/A

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

African (AFR) AF: 0.205 AC: 8499 AN: 41496

American (AMR) AF: 0.120 AC: 1828 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 650 AN: 3464

East Asian (EAS) AF: 0.0480 AC: 249 AN: 5184

South Asian (SAS) AF: 0.172 AC: 828 AN: 4822

European-Finnish (FIN) AF: 0.197 AC: 2084 AN: 10576

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15291 AN: 67968

Other (OTH) AF: 0.195 AC: 411 AN: 2112

Alfa AF: 0.211 Hom.: 9611

Bravo AF: 0.189

Asia WGS AF: 0.104 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.50
PhyloP100		-0.53

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11781985;

hg19: chr8-8589783;