rs11889031

chr2-203934671-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_427213.4(LOC101927840):n.408+1437G>A variant causes a intron, non coding transcript 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: LOC101927840 XR_427213.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.876

Genes affected

LOC101927840 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC101927840	XR_427213.4	n.408+1437G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0466

Gnomad4 NFE AF: 0.0626

Gnomad4 OTH AF: 0.143

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11889031; hg19: chr2-204799394;