12-93247422-T-C

Position:

• chr12-93247422-T-C

Variant summary

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

The NR_040096.1(LOC643339):​n.330-31743A>G 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 0.693 in 151,192 control chromosomes in the GnomAD database, including 36,438 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 0.69 (36438 hom., cov: 28)
• Consequence: LOC643339 NR_040096.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.80

Genes affected

LOC643339 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC643339	NR_040096.1	n.330-31743A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.693 AC: 104709 AN: 151082 Hom.: 36410 Cov.: 28

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.693 AC: 104781 AN: 151192 Hom.: 36438 Cov.: 28 AF XY: 0.692 AC XY: 51039 AN XY: 73764

Gnomad4 AFR AF: 0.713

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.684

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.702

Alfa AF: 0.692 Hom.: 69131

Bravo AF: 0.688

Asia WGS AF: 0.671 AC: 2337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.011
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7973431; hg19: chr12-93641198;