rs841603

chr12-27158549-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000538920.1(ENSG00000256226):n.243+2602C>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 0.491 in 151,946 control chromosomes in the GnomAD database, including 19,496 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 0.49 (19496 hom., cov: 32)
• Consequence: ENST00000538920.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.59 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
	ENST00000538920.1	n.243+2602C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000540595.1	n.116+2602C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74612 AN: 151828 Hom.: 19496 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.491 AC: 74634 AN: 151946 Hom.: 19496 Cov.: 32 AF XY: 0.484 AC XY: 35925 AN XY: 74288

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.494

Alfa AF: 0.525 Hom.: 8074

Bravo AF: 0.470

Asia WGS AF: 0.274 AC: 955 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
Cadd	Benign	15
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs841603; hg19: chr12-27311482;