rs1562771

Positions:

• chr18-77184818-G-A

Variant summary

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

The ENST00000584843.1(ENSG00000265844):​n.96-366G>A 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 0.118 in 152,234 control chromosomes in the GnomAD database, including 1,410 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 0.12 (1410 hom., cov: 32)
• Consequence: ENST00000584843.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 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
	ENST00000584843.1	n.96-366G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17993 AN: 152116 Hom.: 1404 Cov.: 32

Gnomad AFR AF: 0.0290

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.0741

Gnomad SAS AF: 0.0807

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.118 AC: 18013 AN: 152234 Hom.: 1410 Cov.: 32 AF XY: 0.120 AC XY: 8970 AN XY: 74444

Gnomad4 AFR AF: 0.0290

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.0804

Gnomad4 EAS AF: 0.0743

Gnomad4 SAS AF: 0.0814

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.123

Alfa AF: 0.144 Hom.: 877

Bravo AF: 0.105

Asia WGS AF: 0.103 AC: 356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.35
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1562771; hg19: chr18-74896774;