rs4663098

Variant names:

• chr2-127115459-T-C
• rs4663098
• XR_923311.4:n.672-804T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-127115459-T-C
• chr2-127115459-T-G

Variant summary

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

The XR_923311.4(LOC105373605):​n.672-804T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 151,854 control chromosomes in the GnomAD database, including 45,663 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 0.77 (45663 hom., cov: 29)
• Consequence: LOC105373605 XR_923311.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754
• Publications: 20 publications found

Genes affected

LOC105373605 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117369 AN: 151738 Hom.: 45602 Cov.: 29

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.774 AC: 117493 AN: 151854 Hom.: 45663 Cov.: 29 AF XY: 0.771 AC XY: 57158 AN XY: 74170

African (AFR) AF: 0.821 AC: 33974 AN: 41396

American (AMR) AF: 0.728 AC: 11101 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 2464 AN: 3466

East Asian (EAS) AF: 0.616 AC: 3174 AN: 5152

South Asian (SAS) AF: 0.797 AC: 3829 AN: 4804

European-Finnish (FIN) AF: 0.720 AC: 7581 AN: 10522

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.778 AC: 52878 AN: 67956

Other (OTH) AF: 0.750 AC: 1576 AN: 2100

Alfa AF: 0.770 Hom.: 149492

Bravo AF: 0.768

Asia WGS AF: 0.753 AC: 2620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.32
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs4663098; hg19: chr2-127873035;