chr4-4932872-G-C

Variant names:

• chr4-4932872-G-C
• rs4426714
• ENST00000774609.1:n.142-948G>C

Variant summary

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

The NR_125893.1(LOC101928306):​n.354-948G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,976 control chromosomes in the GnomAD database, including 13,322 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 0.41 (13322 hom., cov: 32)
• Consequence: LOC101928306 NR_125893.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437
• Publications: 3 publications found

Genes affected

ENSG00000300857 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_125893.1. 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
	LOC101928306	NR_125893.1		n.354-948G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300857	ENST00000774609.1		n.142-948G>C		intron	N/A
	ENSG00000300857	ENST00000774610.1		n.165-948G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62914 AN: 151858 Hom.: 13310 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.414 AC: 62941 AN: 151976 Hom.: 13322 Cov.: 32 AF XY: 0.420 AC XY: 31190 AN XY: 74258

African (AFR) AF: 0.429 AC: 17777 AN: 41458

American (AMR) AF: 0.433 AC: 6612 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1481 AN: 3472

East Asian (EAS) AF: 0.654 AC: 3369 AN: 5152

South Asian (SAS) AF: 0.386 AC: 1859 AN: 4812

European-Finnish (FIN) AF: 0.428 AC: 4513 AN: 10552

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26054 AN: 67950

Other (OTH) AF: 0.409 AC: 865 AN: 2114

Alfa AF: 0.251 Hom.: 579

Bravo AF: 0.417

Asia WGS AF: 0.450 AC: 1569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.29
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs4426714; hg19: chr4-4934599;