rs714861

Variant names:

• chr4-54088264-G-A
• rs714861
• ENST00000507166.5:c.1018-186661G>A

Variant summary

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

The ENST00000507166.5(ENSG00000282278):​c.1018-186661G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,810 control chromosomes in the GnomAD database, including 14,256 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 0.42 (14256 hom., cov: 31)
• Consequence: ENSG00000282278 ENST00000507166.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 1 publications found

Genes affected

ENSG00000282278 (HGNC:):

CHIC2 (HGNC:1935): (cysteine rich hydrophobic domain 2) This gene encodes a member of the CHIC family of proteins. The encoded protein contains a cysteine-rich hydrophobic (CHIC) motif, and is localized to vesicular structures and the plasma membrane. This gene is associated with some cases of acute myeloid leukemia. [provided by RefSeq, Jul 2008]

MORF4L2P1 (HGNC:20403): (mortality factor 4 like 2 pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507166.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000282278	ENST00000507166.5	TSL:2	c.1018-186661G>A		intron	N/A	ENSP00000423325.1	A0A0B4J203
	ENSG00000298834	ENST00000758259.1		n.126+3517C>T		intron	N/A
	ENSG00000298834	ENST00000758260.1		n.125+3517C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63035 AN: 151692 Hom.: 14218 Cov.: 31

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.416 AC: 63133 AN: 151810 Hom.: 14256 Cov.: 31 AF XY: 0.407 AC XY: 30226 AN XY: 74182

African (AFR) AF: 0.597 AC: 24713 AN: 41364

American (AMR) AF: 0.322 AC: 4921 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1259 AN: 3464

East Asian (EAS) AF: 0.179 AC: 928 AN: 5170

South Asian (SAS) AF: 0.363 AC: 1751 AN: 4820

European-Finnish (FIN) AF: 0.288 AC: 3026 AN: 10510

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25384 AN: 67912

Other (OTH) AF: 0.405 AC: 852 AN: 2102

Alfa AF: 0.394 Hom.: 1981

Bravo AF: 0.421

Asia WGS AF: 0.290 AC: 1012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	1.6
DANN	Benign	0.80
PhyloP100		-0.71
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs714861;

hg19: chr4-54954431;

COSMIC: COSV72264526;

COSMIC: COSV72264526;