rs10496578

chr2-122271461-A-T

Variant summary

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

The ENST00000657880.1(ENSG00000286481):n.704+50542A>T 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 0.0715 in 152,268 control chromosomes in the GnomAD database, including 990 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 0.072 (990 hom., cov: 32)
• Consequence: ENST00000657880.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.809

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 (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373592	XR_001739684.2	n.752+50542A>T		intron_variant, non_coding_transcript_variant
LOC105373592	XR_007087222.1	n.752+50542A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000657880.1	n.704+50542A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0714 AC: 10861 AN: 152150 Hom.: 984 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0422

Gnomad ASJ AF: 0.0418

Gnomad EAS AF: 0.0377

Gnomad SAS AF: 0.0354

Gnomad FIN AF: 0.0125

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.00974

Gnomad OTH AF: 0.0636

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

GnomAD4 genome AF: 0.0715 AC: 10894 AN: 152268 Hom.: 990 Cov.: 32 AF XY: 0.0705 AC XY: 5248 AN XY: 74436

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.0421

Gnomad4 ASJ AF: 0.0418

Gnomad4 EAS AF: 0.0378

Gnomad4 SAS AF: 0.0350

Gnomad4 FIN AF: 0.0125

Gnomad4 NFE AF: 0.00975

Gnomad4 OTH AF: 0.0629

Alfa AF: 0.0456 Hom.: 91

Bravo AF: 0.0803

Asia WGS AF: 0.0490 AC: 171 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	1.6
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496578; hg19: chr2-123029037;