rs2473116

Positions:

• chr10-42641441-G-A

Variant summary

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

The ENST00000649715.3(ENSG00000285884):​n.302+2888G>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 0.274 in 151,990 control chromosomes in the GnomAD database, including 6,934 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 0.27 (6934 hom., cov: 32)
• Consequence: ENST00000649715.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378268	XR_007062125.1	n.579+2178G>A		intron_variant, non_coding_transcript_variant
LOC105378268	XR_007062124.1	n.537+2600G>A		intron_variant, non_coding_transcript_variant
LOC105378268	XR_945898.3	n.249+2888G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000649715.3	n.302+2888G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41596 AN: 151872 Hom.: 6933 Cov.: 32

Gnomad AFR AF: 0.0802

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.274 AC: 41592 AN: 151990 Hom.: 6934 Cov.: 32 AF XY: 0.271 AC XY: 20134 AN XY: 74264

Gnomad4 AFR AF: 0.0800

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.273

Alfa AF: 0.327 Hom.: 1173

Bravo AF: 0.263

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2473116; hg19: chr10-43136889;