rs1443010

Positions:

• chr18-30409800-T-C

Variant summary

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

The ENST00000657542.1(ENSG00000286605):​n.528-2827T>C 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 0.0323 in 152,292 control chromosomes in the GnomAD database, including 206 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 0.032 (206 hom., cov: 32)
• Consequence: ENST00000657542.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.530

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.115 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
	ENST00000657542.1	n.528-2827T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0322 AC: 4899 AN: 152174 Hom.: 201 Cov.: 32

Gnomad AFR AF: 0.0459

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.00893

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0124

Gnomad FIN AF: 0.00480

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00667

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0323 AC: 4919 AN: 152292 Hom.: 206 Cov.: 32 AF XY: 0.0341 AC XY: 2540 AN XY: 74466

Gnomad4 AFR AF: 0.0459

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.00893

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.0126

Gnomad4 FIN AF: 0.00480

Gnomad4 NFE AF: 0.00667

Gnomad4 OTH AF: 0.0308

Alfa AF: 0.0147 Hom.: 88

Bravo AF: 0.0416

Asia WGS AF: 0.0590 AC: 204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.6
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1443010; hg19: chr18-27989766;