11-38183121-T-C

Variant names:

• chr11-38183121-T-C
• rs2169487
• ENST00000822141.1:n.564+17814A>G

Variant summary

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

The ENST00000822141.1(ENSG00000306949):​n.564+17814A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.911 in 152,236 control chromosomes in the GnomAD database, including 64,292 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 0.91 (64292 hom., cov: 33)
• Consequence: ENSG00000306949 ENST00000822141.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486
• Publications: 1 publications found

Genes affected

ENSG00000306949 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.982 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
ENSG00000306949	ENST00000822141.1	n.564+17814A>G		intron_variant	Intron 3 of 3
ENSG00000306949	ENST00000822142.1	n.569-11899A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.912 AC: 138680 AN: 152118 Hom.: 64273 Cov.: 33

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.963

Gnomad ASJ AF: 0.992

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.946

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.911 AC: 138750 AN: 152236 Hom.: 64292 Cov.: 33 AF XY: 0.915 AC XY: 68100 AN XY: 74434

African (AFR) AF: 0.723 AC: 29978 AN: 41488

American (AMR) AF: 0.963 AC: 14732 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.992 AC: 3444 AN: 3472

East Asian (EAS) AF: 0.982 AC: 5087 AN: 5178

South Asian (SAS) AF: 0.945 AC: 4564 AN: 4830

European-Finnish (FIN) AF: 0.996 AC: 10588 AN: 10628

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.988 AC: 67212 AN: 68026

Other (OTH) AF: 0.932 AC: 1971 AN: 2114

Alfa AF: 0.967 Hom.: 39232

Bravo AF: 0.901

Asia WGS AF: 0.944 AC: 3277 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.48
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs2169487; hg19: chr11-38204671;