rs4237559

Variant names:

• chr11-93576281-A-G
• rs4237559
• ENST00000774790.1:n.374+3747T>C

Variant summary

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

The ENST00000774790.1(ENSG00000300871):​n.374+3747T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 151,970 control chromosomes in the GnomAD database, including 18,494 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 0.49 (18494 hom., cov: 31)
• Consequence: ENSG00000300871 ENST00000774790.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 1 publications found

Genes affected

ENSG00000300871 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.585 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
ENSG00000300871	ENST00000774790.1	n.374+3747T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74340 AN: 151852 Hom.: 18472 Cov.: 31

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.490 AC: 74406 AN: 151970 Hom.: 18494 Cov.: 31 AF XY: 0.489 AC XY: 36336 AN XY: 74262

African (AFR) AF: 0.508 AC: 21044 AN: 41438

American (AMR) AF: 0.595 AC: 9082 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1798 AN: 3466

East Asian (EAS) AF: 0.472 AC: 2432 AN: 5154

South Asian (SAS) AF: 0.518 AC: 2495 AN: 4812

European-Finnish (FIN) AF: 0.416 AC: 4389 AN: 10560

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31488 AN: 67952

Other (OTH) AF: 0.461 AC: 975 AN: 2114

Alfa AF: 0.477 Hom.: 8321

Bravo AF: 0.504

Asia WGS AF: 0.472 AC: 1645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.075
DANN	Benign	0.77
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs4237559; hg19: chr11-93309447;