4-66950161-C-G

Variant names:

• chr4-66950161-C-G
• rs1435431
• XR_938847.2:n.345-79314G>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_938847.2(LOC105377262):​n.345-79314G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 151,994 control chromosomes in the GnomAD database, including 5,195 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 0.24 (5195 hom., cov: 32)
• Consequence: LOC105377262 XR_938847.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 1 publications found

Genes affected

LOC105377262 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 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: 0.242 AC: 36740 AN: 151874 Hom.: 5191 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.0688

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.242 AC: 36772 AN: 151994 Hom.: 5195 Cov.: 32 AF XY: 0.242 AC XY: 17997 AN XY: 74284

African (AFR) AF: 0.375 AC: 15540 AN: 41446

American (AMR) AF: 0.155 AC: 2358 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 909 AN: 3470

East Asian (EAS) AF: 0.0686 AC: 355 AN: 5176

South Asian (SAS) AF: 0.346 AC: 1665 AN: 4810

European-Finnish (FIN) AF: 0.210 AC: 2218 AN: 10578

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13052 AN: 67942

Other (OTH) AF: 0.223 AC: 471 AN: 2110

Alfa AF: 0.126 Hom.: 218

Bravo AF: 0.239

Asia WGS AF: 0.200 AC: 697 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	20
DANN	Benign	0.66
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs1435431; hg19: chr4-67815879;