rs11083567

Variant names:

• chr19-40812401-G-A
• rs11083567
• ENST00000601627.1:n.117+10986G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-40812401-G-A
• chr19-40812401-G-C
• chr19-40812401-G-T

Variant summary

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

The ENST00000601627.1(ENSG00000268797):​n.117+10986G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,044 control chromosomes in the GnomAD database, including 3,502 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 0.21 (3502 hom., cov: 32)
• Consequence: ENSG00000268797 ENST00000601627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.883

Genes affected

ENSG00000268797 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000268797	ENST00000601627.1	n.117+10986G>A		intron_variant	Intron 1 of 3	3		ENSP00000469533.1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31425 AN: 151928 Hom.: 3501 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0898

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.207 AC: 31449 AN: 152044 Hom.: 3502 Cov.: 32 AF XY: 0.202 AC XY: 15042 AN XY: 74344

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.0898

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.207

Alfa AF: 0.182 Hom.: 2299

Bravo AF: 0.212

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.60
DANN	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11083567; hg19: chr19-41318306;