rs420017

chr15-89073850-C-T

Variant summary

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

The NR_183882.1(CARMAL):n.405-1446C>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 0.442 in 151,960 control chromosomes in the GnomAD database, including 17,095 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 (17095 hom., cov: 31)
• Consequence: CARMAL NR_183882.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

Genes affected

CARMAL (HGNC:55102): (coronary artery disease region linked MFGE8 regulatory lncRNA)

ABHD2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CARMAL	NR_183882.1	n.405-1446C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CARMAL	ENST00000565938.1	n.180-1446C>T		intron_variant, non_coding_transcript_variant		2
CARMAL	ENST00000668304.1	n.129-1446C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67114 AN: 151840 Hom.: 17094 Cov.: 31

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.442 AC: 67138 AN: 151960 Hom.: 17095 Cov.: 31 AF XY: 0.440 AC XY: 32665 AN XY: 74274

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.461

Alfa AF: 0.549 Hom.: 28137

Bravo AF: 0.415

Asia WGS AF: 0.405 AC: 1409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.62
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs420017; hg19: chr15-89617081;