chr4-74347101-C-T

Variant names:

• chr4-74347101-C-T
• rs1812149
• ENST00000805841.1:n.192-16797G>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.192-16797G>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 151,930 control chromosomes in the GnomAD database, including 9,555 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 (9555 hom., cov: 32)
• Consequence: LOC105377276 NR_188415.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393
• Publications: 9 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=-0.8).
• 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: NR_188415.1. 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.192-16797G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304732	ENST00000805841.1		n.192-16797G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51936 AN: 151814 Hom.: 9532 Cov.: 32

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.264

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: 52018 AN: 151930 Hom.: 9555 Cov.: 32 AF XY: 0.348 AC XY: 25824 AN XY: 74248

African (AFR) AF: 0.443 AC: 18373 AN: 41446

American (AMR) AF: 0.403 AC: 6148 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 946 AN: 3464

East Asian (EAS) AF: 0.466 AC: 2408 AN: 5164

South Asian (SAS) AF: 0.453 AC: 2186 AN: 4826

European-Finnish (FIN) AF: 0.295 AC: 3101 AN: 10526

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

European-Non Finnish (NFE) AF: 0.264 AC: 17904 AN: 67930

Other (OTH) AF: 0.313 AC: 660 AN: 2106

Alfa AF: 0.278 Hom.: 3220

Bravo AF: 0.354

Asia WGS AF: 0.473 AC: 1643 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.7
DANN	Benign	0.51
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs1812149; hg19: chr4-75212818;