4-113395082-T-G

Variant names:

• chr4-113395082-T-G
• rs7685671
• NR_199843.1:n.741-3553A>C

Variant summary

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

The NR_199843.1(LOC105377374):​n.741-3553A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,176 control chromosomes in the GnomAD database, including 32,899 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 0.64 (32899 hom., cov: 33)
• Consequence: LOC105377374 NR_199843.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371
• Publications: 1 publications found

Genes affected

LOC105377374 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_199843.1. 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
	LOC105377374	NR_199843.1		n.741-3553A>C		intron	N/A
	LOC105377374	NR_199847.1		n.493-4261A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97757 AN: 152056 Hom.: 32859 Cov.: 33

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.643 AC: 97845 AN: 152176 Hom.: 32899 Cov.: 33 AF XY: 0.641 AC XY: 47655 AN XY: 74366

African (AFR) AF: 0.855 AC: 35507 AN: 41518

American (AMR) AF: 0.583 AC: 8907 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1709 AN: 3472

East Asian (EAS) AF: 0.452 AC: 2339 AN: 5170

South Asian (SAS) AF: 0.645 AC: 3113 AN: 4826

European-Finnish (FIN) AF: 0.540 AC: 5710 AN: 10572

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38714 AN: 68016

Other (OTH) AF: 0.599 AC: 1267 AN: 2114

Alfa AF: 0.566 Hom.: 11196

Bravo AF: 0.650

Asia WGS AF: 0.564 AC: 1958 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	5.3
DANN	Benign	0.46
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs7685671; hg19: chr4-114316238; COSMIC: COSV53469907;