11-38180741-A-G

Variant names:

• chr11-38180741-A-G
• rs2861126
• ENST00000822141.1:n.564+20194T>C

Variant summary

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

The ENST00000822141.1(ENSG00000306949):​n.564+20194T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.924 in 152,146 control chromosomes in the GnomAD database, including 65,502 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 0.92 (65502 hom., cov: 31)
• Consequence: ENSG00000306949 ENST00000822141.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 0 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=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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+20194T>C		intron_variant	Intron 3 of 3
ENSG00000306949	ENST00000822142.1	n.569-9519T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.924 AC: 140499 AN: 152028 Hom.: 65468 Cov.: 31

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.960

Gnomad ASJ AF: 0.992

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.942

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.941

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

GnomAD4 genome AF: 0.924 AC: 140589 AN: 152146 Hom.: 65502 Cov.: 31 AF XY: 0.926 AC XY: 68864 AN XY: 74402

African (AFR) AF: 0.787 AC: 32635 AN: 41442

American (AMR) AF: 0.961 AC: 14692 AN: 15296

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

East Asian (EAS) AF: 0.982 AC: 5082 AN: 5174

South Asian (SAS) AF: 0.941 AC: 4539 AN: 4822

European-Finnish (FIN) AF: 0.968 AC: 10257 AN: 10594

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.982 AC: 66781 AN: 68030

Other (OTH) AF: 0.941 AC: 1988 AN: 2112

Alfa AF: 0.938 Hom.: 4069

Bravo AF: 0.918

Asia WGS AF: 0.945 AC: 3288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.31
DANN	Benign	0.36
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2861126; hg19: chr11-38202291;