4-54227864-C-G

Variant names:

• chr4-54227864-C-G
• rs1800810
• ENST00000507166.5:c.1018-47061C>G

Variant summary

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

The ENST00000507166.5(ENSG00000282278):​c.1018-47061C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 151,836 control chromosomes in the GnomAD database, including 5,687 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 0.26 (5687 hom., cov: 32)
• Consequence: ENSG00000282278 ENST00000507166.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 14 publications found

Genes affected

ENSG00000282278 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.357 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
ENSG00000282278	ENST00000507166.5	c.1018-47061C>G		intron_variant	Intron 12 of 23	2		ENSP00000423325.1

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39666 AN: 151718 Hom.: 5671 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.262 AC: 39738 AN: 151836 Hom.: 5687 Cov.: 32 AF XY: 0.261 AC XY: 19387 AN XY: 74160

African (AFR) AF: 0.362 AC: 14965 AN: 41390

American (AMR) AF: 0.335 AC: 5114 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 349 AN: 3472

East Asian (EAS) AF: 0.199 AC: 1016 AN: 5112

South Asian (SAS) AF: 0.251 AC: 1209 AN: 4818

European-Finnish (FIN) AF: 0.207 AC: 2177 AN: 10520

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14249 AN: 67960

Other (OTH) AF: 0.228 AC: 481 AN: 2108

Alfa AF: 0.113 Hom.: 158

Bravo AF: 0.276

Asia WGS AF: 0.266 AC: 927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.4
DANN	Benign	0.58
PhyloP100		0.36
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1800810; hg19: chr4-55094031;