chr4-23483641-T-G

Variant names:

• chr4-23483641-T-G
• rs6857002
• XR_007058437.1:n.3134-20366T>G

Variant summary

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

The XR_007058437.1(LOC105374524):​n.3134-20366T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,024 control chromosomes in the GnomAD database, including 7,446 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 0.30 (7446 hom., cov: 32)
• Consequence: LOC105374524 XR_007058437.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 3 publications found

Genes affected

LOC105374524 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45995 AN: 151906 Hom.: 7416 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.0989

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.303 AC: 46091 AN: 152024 Hom.: 7446 Cov.: 32 AF XY: 0.306 AC XY: 22745 AN XY: 74330

African (AFR) AF: 0.408 AC: 16882 AN: 41420

American (AMR) AF: 0.286 AC: 4372 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 839 AN: 3472

East Asian (EAS) AF: 0.0988 AC: 511 AN: 5174

South Asian (SAS) AF: 0.380 AC: 1830 AN: 4822

European-Finnish (FIN) AF: 0.291 AC: 3079 AN: 10578

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17657 AN: 67968

Other (OTH) AF: 0.298 AC: 628 AN: 2106

Alfa AF: 0.275 Hom.: 11323

Bravo AF: 0.305

Asia WGS AF: 0.252 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.6
DANN	Benign	0.33
PhyloP100		0.0010

Splicing

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

Other links and lift over

dbSNP: rs6857002; hg19: chr4-23485264;