rs2226844

Positions:

• chr11-87576547-G-A
• chr11-87576547-G-C

Variant summary

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

The XR_002957260.2(LOC107984361):​n.466+23178G>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 0.633 in 151,944 control chromosomes in the GnomAD database, including 30,895 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 0.63 (30895 hom., cov: 32)
• Consequence: LOC107984361 XR_002957260.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810

Genes affected

LOC107984361 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984361	XR_002957260.2	n.466+23178G>A		intron_variant, non_coding_transcript_variant
LOC107984361	XR_001748316.2	n.389+23178G>A		intron_variant, non_coding_transcript_variant
LOC107984361	XR_002957261.2	n.389+23178G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96079 AN: 151824 Hom.: 30855 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.633 AC: 96175 AN: 151944 Hom.: 30895 Cov.: 32 AF XY: 0.624 AC XY: 46351 AN XY: 74258

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.656

Alfa AF: 0.629 Hom.: 9277

Bravo AF: 0.647

Asia WGS AF: 0.490 AC: 1703 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.93
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2226844; hg19: chr11-87287439;