rs10496009

Positions:

• chr2-52805408-A-G

Variant summary

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

The ENST00000421575.6(ENSG00000228033):​n.208-72631T>C 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 0.0539 in 152,158 control chromosomes in the GnomAD database, including 503 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 0.054 (503 hom., cov: 32)
• Consequence: ENST00000421575.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369165	XR_002959384.2	n.172-78590T>C		intron_variant, non_coding_transcript_variant
LOC105369165	XR_001739464.3	n.329-72631T>C		intron_variant, non_coding_transcript_variant
LOC105369165	XR_002959385.2	n.329-10552T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000421575.6	n.208-72631T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000443237.1	n.120-78590T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000668945.1	n.220-78590T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0538 AC: 8181 AN: 152040 Hom.: 503 Cov.: 32

Gnomad AFR AF: 0.0857

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.0211

Gnomad FIN AF: 0.0851

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.00528

Gnomad OTH AF: 0.0617

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

GnomAD4 genome AF: 0.0539 AC: 8199 AN: 152158 Hom.: 503 Cov.: 32 AF XY: 0.0584 AC XY: 4348 AN XY: 74396

Gnomad4 AFR AF: 0.0858

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.0167

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.0207

Gnomad4 FIN AF: 0.0851

Gnomad4 NFE AF: 0.00528

Gnomad4 OTH AF: 0.0611

Alfa AF: 0.0207 Hom.: 169

Bravo AF: 0.0612

Asia WGS AF: 0.128 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.34
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496009; hg19: chr2-53032546;