chr11-93575874-A-G

Variant names:

• chr11-93575874-A-G
• rs4753480
• ENST00000774790.1:n.374+4154T>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+4154T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,980 control chromosomes in the GnomAD database, including 16,221 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 0.46 (16221 hom., cov: 32)
• Consequence: ENSG00000300871 ENST00000774790.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 4 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.571 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+4154T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69454 AN: 151862 Hom.: 16204 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.457 AC: 69500 AN: 151980 Hom.: 16221 Cov.: 32 AF XY: 0.458 AC XY: 34016 AN XY: 74268

African (AFR) AF: 0.398 AC: 16494 AN: 41442

American (AMR) AF: 0.581 AC: 8876 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1798 AN: 3468

East Asian (EAS) AF: 0.463 AC: 2393 AN: 5170

South Asian (SAS) AF: 0.518 AC: 2498 AN: 4826

European-Finnish (FIN) AF: 0.414 AC: 4367 AN: 10536

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31451 AN: 67944

Other (OTH) AF: 0.438 AC: 924 AN: 2110

Alfa AF: 0.471 Hom.: 9719

Bravo AF: 0.467

Asia WGS AF: 0.463 AC: 1614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.57
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs4753480; hg19: chr11-93309040;