chr4-107571209-C-T

Variant names:

• chr4-107571209-C-T
• rs1355990
• XR_939059.3:n.130+7800G>A

Variant summary

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

The XR_939059.3(LOC105377358):​n.130+7800G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 151,848 control chromosomes in the GnomAD database, including 33,958 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 0.66 (33958 hom., cov: 31)
• Consequence: LOC105377358 XR_939059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 0 publications found

Genes affected

LOC105377358 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.665 AC: 100870 AN: 151730 Hom.: 33911 Cov.: 31

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.665 AC: 100968 AN: 151848 Hom.: 33958 Cov.: 31 AF XY: 0.661 AC XY: 49052 AN XY: 74222

African (AFR) AF: 0.760 AC: 31534 AN: 41494

American (AMR) AF: 0.632 AC: 9639 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2198 AN: 3460

East Asian (EAS) AF: 0.515 AC: 2656 AN: 5156

South Asian (SAS) AF: 0.477 AC: 2296 AN: 4814

European-Finnish (FIN) AF: 0.664 AC: 7014 AN: 10568

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43422 AN: 67800

Other (OTH) AF: 0.657 AC: 1387 AN: 2110

Alfa AF: 0.650 Hom.: 12338

Bravo AF: 0.671

Asia WGS AF: 0.488 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	9.0
DANN	Benign	0.62
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs1355990; hg19: chr4-108492366;