4-74347587-G-T

Variant names:

• chr4-74347587-G-T
• rs12646908
• ENST00000805841.1:n.192-17283C>A

Variant summary

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

The NR_188415.1(LOC105377276):​n.192-17283C>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 151,742 control chromosomes in the GnomAD database, including 9,528 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 (9528 hom., cov: 31)
• Consequence: LOC105377276 NR_188415.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_188415.1. 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
	LOC105377276	NR_188415.1		n.192-17283C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304732	ENST00000805841.1		n.192-17283C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51861 AN: 151624 Hom.: 9505 Cov.: 31

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.342 AC: 51943 AN: 151742 Hom.: 9528 Cov.: 31 AF XY: 0.348 AC XY: 25785 AN XY: 74136

African (AFR) AF: 0.443 AC: 18338 AN: 41370

American (AMR) AF: 0.403 AC: 6130 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 947 AN: 3462

East Asian (EAS) AF: 0.466 AC: 2402 AN: 5158

South Asian (SAS) AF: 0.454 AC: 2176 AN: 4790

European-Finnish (FIN) AF: 0.295 AC: 3106 AN: 10534

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.264 AC: 17891 AN: 67894

Other (OTH) AF: 0.314 AC: 662 AN: 2108

Alfa AF: 0.314 Hom.: 1021

Bravo AF: 0.354

Asia WGS AF: 0.473 AC: 1647 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	1.5
DANN	Benign	0.40
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs12646908; hg19: chr4-75213304;