rs4128691

Variant names:

• chr3-72300712-C-T
• rs4128691
• XR_001740748.3:n.405+1937G>A

Variant summary

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

The XR_940959.2(LOC105377158):​n.405+1937G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,108 control chromosomes in the GnomAD database, including 6,848 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 0.29 (6848 hom., cov: 32)
• Consequence: LOC105377158 XR_940959.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 2 publications found

Genes affected

LOC105377158 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 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: 0.295 AC: 44785 AN: 151990 Hom.: 6851 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.295 AC: 44804 AN: 152108 Hom.: 6848 Cov.: 32 AF XY: 0.293 AC XY: 21763 AN XY: 74352

African (AFR) AF: 0.368 AC: 15236 AN: 41446

American (AMR) AF: 0.307 AC: 4688 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 917 AN: 3470

East Asian (EAS) AF: 0.408 AC: 2107 AN: 5166

South Asian (SAS) AF: 0.296 AC: 1426 AN: 4820

European-Finnish (FIN) AF: 0.207 AC: 2189 AN: 10594

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17239 AN: 68016

Other (OTH) AF: 0.286 AC: 604 AN: 2110

Alfa AF: 0.264 Hom.: 4717

Bravo AF: 0.307

Asia WGS AF: 0.338 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.61
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4128691;

hg19: chr3-72349863;