chr2-219918601-C-T

Variant names:

• chr2-219918601-C-T
• rs4672960
• XR_001739233.2:n.289+657C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_923927.3(LOC105373890):​n.278+657C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,092 control chromosomes in the GnomAD database, including 5,861 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 0.27 (5861 hom., cov: 33)
• Consequence: LOC105373890 XR_923927.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367

Genes affected

LOC105373890 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373890	XR_001739233.2	n.289+657C>T		intron_variant	Intron 2 of 2
LOC105373890	XR_923927.3	n.278+657C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40939 AN: 151972 Hom.: 5865 Cov.: 33

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.0937

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.269 AC: 40937 AN: 152092 Hom.: 5861 Cov.: 33 AF XY: 0.267 AC XY: 19857 AN XY: 74328

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.0937

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.281

Alfa AF: 0.297 Hom.: 14130

Bravo AF: 0.258

Asia WGS AF: 0.152 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.17
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4672960; hg19: chr2-220783322;