rs11894053

Variant names:

• chr2-42002405-A-G
• rs11894053
• ENST00000777407.1:n.237-18616T>C

Variant summary

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

The ENST00000777407.1(ENSG00000226398):​n.237-18616T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,180 control chromosomes in the GnomAD database, including 5,392 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 0.26 (5392 hom., cov: 33)
• Consequence: ENSG00000226398 ENST00000777407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 4 publications found

Genes affected

ENSG00000226398 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 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
ENSG00000226398	ENST00000777407.1	n.237-18616T>C		intron_variant	Intron 1 of 2
ENSG00000226398	ENST00000777408.1	n.218-18695T>C		intron_variant	Intron 1 of 2
ENSG00000226398	ENST00000777409.1	n.339-15097T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39125 AN: 152062 Hom.: 5388 Cov.: 33

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.257 AC: 39158 AN: 152180 Hom.: 5392 Cov.: 33 AF XY: 0.260 AC XY: 19347 AN XY: 74414

African (AFR) AF: 0.323 AC: 13405 AN: 41500

American (AMR) AF: 0.187 AC: 2857 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1114 AN: 3470

East Asian (EAS) AF: 0.102 AC: 531 AN: 5190

South Asian (SAS) AF: 0.283 AC: 1363 AN: 4824

European-Finnish (FIN) AF: 0.308 AC: 3260 AN: 10584

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15552 AN: 68000

Other (OTH) AF: 0.265 AC: 561 AN: 2114

Alfa AF: 0.234 Hom.: 733

Bravo AF: 0.251

Asia WGS AF: 0.205 AC: 716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.4
DANN	Benign	0.78
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs11894053; hg19: chr2-42229545;