chr4-73877974-C-G

Variant names:

• chr4-73877974-C-G
• rs2115691
• ENST00000791548.1:n.122+4036C>G

Variant summary

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

The ENST00000791548.1(ENSG00000303067):​n.122+4036C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 151,958 control chromosomes in the GnomAD database, including 17,076 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 (17076 hom., cov: 32)
• Consequence: ENSG00000303067 ENST00000791548.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.715
• Publications: 6 publications found

Genes affected

ENSG00000303067 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791548.1. 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
	ENSG00000303067	ENST00000791548.1		n.122+4036C>G		intron	N/A
	ENSG00000303067	ENST00000791549.1		n.65-3813C>G		intron	N/A
	ENSG00000303067	ENST00000791550.1		n.59+4036C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63922 AN: 151840 Hom.: 17014 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.421 AC: 64042 AN: 151958 Hom.: 17076 Cov.: 32 AF XY: 0.422 AC XY: 31332 AN XY: 74278

African (AFR) AF: 0.748 AC: 30997 AN: 41442

American (AMR) AF: 0.459 AC: 7004 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1359 AN: 3468

East Asian (EAS) AF: 0.437 AC: 2255 AN: 5158

South Asian (SAS) AF: 0.366 AC: 1765 AN: 4818

European-Finnish (FIN) AF: 0.260 AC: 2742 AN: 10566

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16629 AN: 67928

Other (OTH) AF: 0.426 AC: 900 AN: 2112

Alfa AF: 0.183 Hom.: 426

Bravo AF: 0.453

Asia WGS AF: 0.425 AC: 1478 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	4.5
DANN	Benign	0.38
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs2115691; hg19: chr4-74743691;