4-74342802-G-T

Variant names:

• chr4-74342802-G-T
• rs2125398
• ENST00000805841.1:n.192-12498C>A

Variant summary

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

The ENST00000805841.1(ENSG00000304732):​n.192-12498C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 151,966 control chromosomes in the GnomAD database, including 9,547 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 0.34 (9547 hom., cov: 32)
• Consequence: ENSG00000304732 ENST00000805841.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 4 publications found

Genes affected

ENSG00000304732 (HGNC:58817):

LOC105377276 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000805841.1. 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
	LOC105377276	NR_188415.1		n.192-12498C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304732	ENST00000805841.1		n.192-12498C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51927 AN: 151848 Hom.: 9524 Cov.: 32

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.342 AC: 52009 AN: 151966 Hom.: 9547 Cov.: 32 AF XY: 0.348 AC XY: 25809 AN XY: 74270

African (AFR) AF: 0.443 AC: 18349 AN: 41424

American (AMR) AF: 0.402 AC: 6145 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 945 AN: 3466

East Asian (EAS) AF: 0.466 AC: 2404 AN: 5158

South Asian (SAS) AF: 0.452 AC: 2180 AN: 4818

European-Finnish (FIN) AF: 0.296 AC: 3124 AN: 10556

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17910 AN: 67956

Other (OTH) AF: 0.313 AC: 661 AN: 2110

Alfa AF: 0.294 Hom.: 17060

Bravo AF: 0.354

Asia WGS AF: 0.473 AC: 1649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.76
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2125398; hg19: chr4-75208519;