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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773540.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300710	ENST00000773540.1		n.277+1437G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11889031;

hg19: chr2-204799394;