rs10496584

Positions:

• chr2-122368903-A-G

Variant summary

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

The ENST00000657880.1(ENSG00000286481):​n.704+147984A>G 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 0.159 in 152,210 control chromosomes in the GnomAD database, including 2,433 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 0.16 (2433 hom., cov: 32)
• Consequence: ENST00000657880.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.587

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373592	XR_001739684.2	n.753-24060A>G		intron_variant, non_coding_transcript_variant
LOC105373592	XR_007087222.1	n.753-24060A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000657880.1	n.704+147984A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24124 AN: 152092 Hom.: 2420 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.159 AC: 24173 AN: 152210 Hom.: 2433 Cov.: 32 AF XY: 0.163 AC XY: 12131 AN XY: 74414

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.175

Alfa AF: 0.154 Hom.: 381

Bravo AF: 0.172

Asia WGS AF: 0.367 AC: 1274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496584; hg19: chr2-123126479;