rs10777477

Positions:

• chr12-93187914-C-A

Variant summary

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

The NR_040096.1(LOC643339):​n.427+27668G>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 0.198 in 152,012 control chromosomes in the GnomAD database, including 3,407 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 (3407 hom., cov: 32)
• Consequence: LOC643339 NR_040096.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC643339	NR_040096.1	n.427+27668G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000549930.1	n.98+27668G>T		intron_variant, non_coding_transcript_variant		5
	ENST00000547432.1	n.316+2353G>T		intron_variant, non_coding_transcript_variant		3
	ENST00000652973.1	n.245+2353G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30118 AN: 151892 Hom.: 3396 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.0769

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.198 AC: 30163 AN: 152012 Hom.: 3407 Cov.: 32 AF XY: 0.199 AC XY: 14752 AN XY: 74298

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.193

Alfa AF: 0.173 Hom.: 2329

Bravo AF: 0.201

Asia WGS AF: 0.140 AC: 487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.39
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10777477; hg19: chr12-93581690;