rs4876377

Variant names:

• chr8-117474750-C-T
• rs4876377
• ENST00000751876.1:n.273-2422G>A

Variant summary

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

The ENST00000751876.1(ENSG00000297933):​n.273-2422G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,140 control chromosomes in the GnomAD database, including 4,411 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 0.21 (4411 hom., cov: 32)
• Consequence: ENSG00000297933 ENST00000751876.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 1 publications found

Genes affected

ENSG00000297933 (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 (NFE) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751876.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297933	ENST00000751876.1		n.273-2422G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32562 AN: 152022 Hom.: 4413 Cov.: 32

Gnomad AFR AF: 0.0662

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.0649

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.214 AC: 32561 AN: 152140 Hom.: 4411 Cov.: 32 AF XY: 0.210 AC XY: 15628 AN XY: 74366

African (AFR) AF: 0.0661 AC: 2747 AN: 41560

American (AMR) AF: 0.203 AC: 3105 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1208 AN: 3468

East Asian (EAS) AF: 0.0651 AC: 337 AN: 5178

South Asian (SAS) AF: 0.262 AC: 1265 AN: 4826

European-Finnish (FIN) AF: 0.218 AC: 2307 AN: 10562

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20662 AN: 67956

Other (OTH) AF: 0.229 AC: 484 AN: 2112

Alfa AF: 0.250 Hom.: 662

Bravo AF: 0.204

Asia WGS AF: 0.170 AC: 593 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.35
PhyloP100		0.064

Splicing

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: rs4876377;

hg19: chr8-118486989;