rs2421027

chr10-122444132-A-G

Variant summary

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

The ENST00000650300.1(ENSG00000285955):n.1853-7500T>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 0.0933 in 151,982 control chromosomes in the GnomAD database, including 792 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 0.093 (792 hom., cov: 32)
• Consequence: ENST00000650300.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650300.1	n.1853-7500T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0934 AC: 14190 AN: 151866 Hom.: 793 Cov.: 32

Gnomad AFR AF: 0.0624

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0944

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0658

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0933 AC: 14183 AN: 151982 Hom.: 792 Cov.: 32 AF XY: 0.0913 AC XY: 6783 AN XY: 74320

Gnomad4 AFR AF: 0.0623

Gnomad4 AMR AF: 0.0942

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.0658

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.103

Alfa AF: 0.110 Hom.: 460

Bravo AF: 0.0901

Asia WGS AF: 0.0810 AC: 277 AN: 3416

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	6.9
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2421027; hg19: chr10-124203648;