rs502943

Variant names:

• chr11-56812140-T-A
• rs502943
• ENST00000378368.4:n.128+7441A>T

Variant summary

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

The ENST00000378368.4(ENSG00000290749):​n.128+7441A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 151,422 control chromosomes in the GnomAD database, including 32,266 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 0.65 (32266 hom., cov: 31)
• Consequence: ENSG00000290749 ENST00000378368.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.910
• Publications: 0 publications found

Genes affected

ENSG00000290749 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.792 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
ENSG00000290749	ENST00000378368.4	n.128+7441A>T		intron_variant	Intron 1 of 2	6
ENSG00000290749	ENST00000531887.1	n.67+7441A>T		intron_variant	Intron 1 of 1	6
ENSG00000290749	ENST00000627642.1	n.322+7961A>T		intron_variant	Intron 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98437 AN: 151304 Hom.: 32221 Cov.: 31

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.651 AC: 98544 AN: 151422 Hom.: 32266 Cov.: 31 AF XY: 0.659 AC XY: 48733 AN XY: 73970

African (AFR) AF: 0.671 AC: 27781 AN: 41390

American (AMR) AF: 0.646 AC: 9796 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1903 AN: 3458

East Asian (EAS) AF: 0.787 AC: 4025 AN: 5114

South Asian (SAS) AF: 0.813 AC: 3911 AN: 4808

European-Finnish (FIN) AF: 0.757 AC: 8005 AN: 10572

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41129 AN: 67618

Other (OTH) AF: 0.641 AC: 1344 AN: 2096

Alfa AF: 0.623 Hom.: 3685

Bravo AF: 0.639

Asia WGS AF: 0.805 AC: 2800 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.8
DANN	Benign	0.38
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs502943; hg19: chr11-56579616;