rs11889031

Variant names:

• chr2-203934671-C-T
• rs11889031
• ENST00000773540.1:n.277+1437G>A

Variant summary

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

The ENST00000773540.1(ENSG00000300710):​n.277+1437G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,110 control chromosomes in the GnomAD database, including 2,956 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 0.15 (2956 hom., cov: 32)
• Consequence: ENSG00000300710 ENST00000773540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.876
• Publications: 11 publications found

Genes affected

ENSG00000300710 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927840	XR_427213.4	n.408+1437G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300710	ENST00000773540.1	n.277+1437G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23328 AN: 151992 Hom.: 2942 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0466

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0626

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.154 AC: 23384 AN: 152110 Hom.: 2956 Cov.: 32 AF XY: 0.154 AC XY: 11456 AN XY: 74382

African (AFR) AF: 0.334 AC: 13842 AN: 41434

American (AMR) AF: 0.117 AC: 1788 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 505 AN: 3466

East Asian (EAS) AF: 0.280 AC: 1449 AN: 5178

South Asian (SAS) AF: 0.125 AC: 601 AN: 4818

European-Finnish (FIN) AF: 0.0466 AC: 494 AN: 10592

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0626 AC: 4259 AN: 68010

Other (OTH) AF: 0.143 AC: 303 AN: 2114

Alfa AF: 0.0985 Hom.: 219

Bravo AF: 0.168

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.19
DANN	Benign	0.43
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs11889031; hg19: chr2-204799394;