rs1075470

chr18-78911085-G-Achr18-78911085-G-Cchr18-78911085-G-T

Variant summary

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

The ENST00000578030.1(ENSG00000266586):n.58-2335C>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 0.542 in 152,050 control chromosomes in the GnomAD database, including 24,256 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 0.54 (24256 hom., cov: 34)
• Consequence: ENST00000578030.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372224	XR_935678.3	n.898-2335C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000578030.1	n.58-2335C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82438 AN: 151932 Hom.: 24257 Cov.: 34

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.542 AC: 82462 AN: 152050 Hom.: 24256 Cov.: 34 AF XY: 0.539 AC XY: 40040 AN XY: 74296

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.570

Alfa AF: 0.648 Hom.: 59528

Bravo AF: 0.524

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.76
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1075470; hg19: chr18-76671085;