rs2156646

Variant names:

• chr18-77234704-G-A
• rs2156646
• ENST00000584843.1:n.503+311G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-77234704-G-A
• chr18-77234704-G-C

Variant summary

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

The ENST00000584843.1(ENSG00000265844):​n.503+311G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,218 control chromosomes in the GnomAD database, including 2,360 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 0.17 (2360 hom., cov: 33)
• Consequence: ENSG00000265844 ENST00000584843.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25
• Publications: 3 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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000584843.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000265844	ENST00000584843.1	TSL:4	n.503+311G>A		intron	N/A
	ENSG00000309801	ENST00000844037.1		n.162+16144C>T		intron	N/A
	ENSG00000309801	ENST00000844038.1		n.118+16097C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26196 AN: 152100 Hom.: 2364 Cov.: 33

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.0681

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.172 AC: 26201 AN: 152218 Hom.: 2360 Cov.: 33 AF XY: 0.173 AC XY: 12865 AN XY: 74416

African (AFR) AF: 0.141 AC: 5859 AN: 41530

American (AMR) AF: 0.146 AC: 2237 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 864 AN: 3468

East Asian (EAS) AF: 0.0679 AC: 352 AN: 5184

South Asian (SAS) AF: 0.202 AC: 972 AN: 4818

European-Finnish (FIN) AF: 0.230 AC: 2432 AN: 10596

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12958 AN: 68020

Other (OTH) AF: 0.171 AC: 362 AN: 2112

Alfa AF: 0.148 Hom.: 482

Bravo AF: 0.163

Asia WGS AF: 0.123 AC: 428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.48
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs2156646; hg19: chr18-74946660;