rs10497650

Positions:

• chr2-184358308-A-G

Variant summary

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

The ENST00000671393.1(ENSG00000286980):​n.550-21850A>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 0.009 in 152,144 control chromosomes in the GnomAD database, including 25 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 0.0090 (25 hom., cov: 32)
• Consequence: ENST00000671393.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.96

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724340	XR_001739819.1	n.318+25415A>G		intron_variant, non_coding_transcript_variant
LOC105373776	XR_923650.3	n.191+2027T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000671393.1	n.550-21850A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00901 AC: 1369 AN: 152026 Hom.: 25 Cov.: 32

Gnomad AFR AF: 0.00545

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.00216

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.0724

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.0116

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00696

Gnomad OTH AF: 0.00720

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

GnomAD4 genome AF: 0.00900 AC: 1369 AN: 152144 Hom.: 25 Cov.: 32 AF XY: 0.00948 AC XY: 705 AN XY: 74360

Gnomad4 AFR AF: 0.00553

Gnomad4 AMR AF: 0.00216

Gnomad4 ASJ AF: 0.00115

Gnomad4 EAS AF: 0.0720

Gnomad4 SAS AF: 0.0151

Gnomad4 FIN AF: 0.0116

Gnomad4 NFE AF: 0.00696

Gnomad4 OTH AF: 0.00760

Alfa AF: 0.00656 Hom.: 1

Bravo AF: 0.00867

Asia WGS AF: 0.0300 AC: 102 AN: 3412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.8
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497650; hg19: chr2-185223035;