12-121189655-A-G

Position:

• chr12-121189655-A-G

Variant summary

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

The ENST00000652651.1(ENSG00000286248):​n.1077+746T>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 0.199 in 151,914 control chromosomes in the GnomAD database, including 3,280 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 (3280 hom., cov: 31)
• Consequence: ENST00000652651.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370032	XR_001749352.3	n.327+13843T>C		intron_variant, non_coding_transcript_variant
LOC105370032	XR_001749353.3	n.268+13843T>C		intron_variant, non_coding_transcript_variant
LOC105370032	XR_945459.4	n.304+13843T>C		intron_variant, non_coding_transcript_variant
LOC105370032	XR_945460.4	n.298+13843T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000652651.1	n.1077+746T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30149 AN: 151796 Hom.: 3278 Cov.: 31

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0647

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.199 AC: 30163 AN: 151914 Hom.: 3280 Cov.: 31 AF XY: 0.194 AC XY: 14371 AN XY: 74248

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.0643

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.191

Alfa AF: 0.176 Hom.: 3363

Bravo AF: 0.194

Asia WGS AF: 0.121 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.2
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1718161; hg19: chr12-121627458;