rs4658673

Variant names:

• chr1-244879010-G-A
• rs4658673
• XM_047439568.1:c.217-14279C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-244879010-G-A
• chr1-244879010-G-C

Variant summary

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

The XM_047439568.1(LOC124904588):​c.217-14279C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 151,236 control chromosomes in the GnomAD database, including 2,634 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 0.18 (2634 hom., cov: 30)
• Consequence: LOC124904588 XM_047439568.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 3 publications found

Genes affected

LOC124904588 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 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: 0.181 AC: 27382 AN: 151146 Hom.: 2640 Cov.: 30

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.181 AC: 27377 AN: 151236 Hom.: 2634 Cov.: 30 AF XY: 0.184 AC XY: 13562 AN XY: 73802

African (AFR) AF: 0.114 AC: 4700 AN: 41228

American (AMR) AF: 0.193 AC: 2927 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 778 AN: 3464

East Asian (EAS) AF: 0.228 AC: 1172 AN: 5138

South Asian (SAS) AF: 0.191 AC: 914 AN: 4794

European-Finnish (FIN) AF: 0.249 AC: 2566 AN: 10320

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.203 AC: 13761 AN: 67824

Other (OTH) AF: 0.162 AC: 340 AN: 2094

Alfa AF: 0.188 Hom.: 8357

Bravo AF: 0.170

Asia WGS AF: 0.170 AC: 595 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	1.1
DANN	Benign	0.80
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4658673; hg19: chr1-245042312;