rs2632208

chr12-76607071-T-Cchr12-76607071-T-G

Variant summary

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

The ENST00000702157.1(ENSG00000257526):n.485-8232T>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 0.197 in 151,992 control chromosomes in the GnomAD database, including 3,350 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 0.20 (3350 hom., cov: 32)
• Consequence: ENST00000702157.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.811

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369850	XR_945113.4	n.453-8232T>C		intron_variant, non_coding_transcript_variant
LOC105369850	XR_001749220.2	n.397-8232T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000702157.1	n.485-8232T>C		intron_variant, non_coding_transcript_variant
	ENST00000551082.2	n.122-8232T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29889 AN: 151874 Hom.: 3335 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.197 AC: 29947 AN: 151992 Hom.: 3350 Cov.: 32 AF XY: 0.200 AC XY: 14853 AN XY: 74270

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.187

Alfa AF: 0.165 Hom.: 1089

Bravo AF: 0.196

Asia WGS AF: 0.332 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.31
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: rs2632208; hg19: chr12-77000851;