rs10496200

chr2-76116064-T-C

Variant summary

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

The ENST00000670606.1(ENSG00000287474):n.832+33372T>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 0.179 in 152,128 control chromosomes in the GnomAD database, including 2,952 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 0.18 (2952 hom., cov: 32)
• Consequence: ENST00000670606.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.768

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 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
	ENST00000670606.1	n.832+33372T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27220 AN: 152010 Hom.: 2932 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.179 AC: 27288 AN: 152128 Hom.: 2952 Cov.: 32 AF XY: 0.184 AC XY: 13651 AN XY: 74362

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.168

Alfa AF: 0.136 Hom.: 3617

Bravo AF: 0.190

Asia WGS AF: 0.340 AC: 1180 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	5.4
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496200; hg19: chr2-76343190;