rs10932886

Positions:

• chr2-220855368-G-A
• chr2-220855368-G-T

Variant summary

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

The ENST00000658049.1(ENSG00000224819):​n.660-367G>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 0.289 in 152,040 control chromosomes in the GnomAD database, including 6,652 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 0.29 (6652 hom., cov: 32)
• Consequence: ENST00000658049.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985990	XR_001739902.1	n.276-367G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000658049.1	n.660-367G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43958 AN: 151920 Hom.: 6655 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.289 AC: 43965 AN: 152040 Hom.: 6652 Cov.: 32 AF XY: 0.280 AC XY: 20814 AN XY: 74316

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.312

Alfa AF: 0.317 Hom.: 12601

Bravo AF: 0.288

Asia WGS AF: 0.210 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.014
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10932886; hg19: chr2-221720088;