12-57431587-C-T

Position:

• chr12-57431587-C-T

Variant summary

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

The ENST00000547552.1(R3HDM2-DT):​n.315+157C>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 0.436 in 151,978 control chromosomes in the GnomAD database, including 15,215 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 0.44 (15215 hom., cov: 32)
• Consequence: R3HDM2-DT ENST00000547552.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

Genes affected

R3HDM2-DT (HGNC:55457): (R3HDM2 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
R3HDM2-DT	ENST00000547552.1	n.315+157C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66146 AN: 151860 Hom.: 15194 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.436 AC: 66194 AN: 151978 Hom.: 15215 Cov.: 32 AF XY: 0.442 AC XY: 32836 AN XY: 74270

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.411

Alfa AF: 0.458 Hom.: 3937

Bravo AF: 0.425

Asia WGS AF: 0.457 AC: 1592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	2.5
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs543410; hg19: chr12-57825370;