rs1562771

Variant names:

• chr18-77184818-G-A
• rs1562771
• ENST00000584843.1:n.96-366G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000584843.1(ENSG00000265844):​n.96-366G>A variant causes a intron 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: ENSG00000265844 ENST00000584843.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 1 publications found

Genes affected

ENSG00000265844 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000265844	ENST00000584843.1	n.96-366G>A		intron_variant	Intron 1 of 4	4
ENSG00000265844	ENST00000843890.1	n.301-366G>A		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.0290 AC: 1203 AN: 41548

American (AMR) AF: 0.123 AC: 1887 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0804 AC: 279 AN: 3468

East Asian (EAS) AF: 0.0743 AC: 385 AN: 5184

South Asian (SAS) AF: 0.0814 AC: 393 AN: 4828

European-Finnish (FIN) AF: 0.224 AC: 2367 AN: 10586

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.164 AC: 11153 AN: 68006

Other (OTH) AF: 0.123 AC: 261 AN: 2114

Alfa AF: 0.139 Hom.: 1170

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
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1562771; hg19: chr18-74896774;