rs4761708

chr12-93358310-C-T

Variant summary

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

The NR_040096.1(LOC643339):n.300+19127G>A 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 0.235 in 151,998 control chromosomes in the GnomAD database, including 4,294 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 0.23 (4294 hom., cov: 31)
• Consequence: LOC643339 NR_040096.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.908

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC643339	NR_040096.1	n.300+19127G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000548890.2	n.317+19127G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000549806.1	n.272+19127G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000552835.5	n.281-18574G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000702599.1	n.295-18574G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35660 AN: 151880 Hom.: 4280 Cov.: 31

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.235 AC: 35679 AN: 151998 Hom.: 4294 Cov.: 31 AF XY: 0.237 AC XY: 17612 AN XY: 74280

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.220

Alfa AF: 0.235 Hom.: 7296

Bravo AF: 0.236

Asia WGS AF: 0.225 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	4.4
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: rs4761708; hg19: chr12-93752086;