2-221608107-C-T

Variant names:

• chr2-221608107-C-T
• rs925949
• XR_923939.2:n.140+2174G>A

Variant summary

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

The XR_923939.2(LOC105373897):​n.140+2174G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 147,014 control chromosomes in the GnomAD database, including 15,132 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 0.45 (15132 hom., cov: 23)
• Consequence: LOC105373897 XR_923939.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.533

Genes affected

LOC105373897 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373897	XR_923939.2	n.140+2174G>A		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.447 AC: 65680 AN: 146914 Hom.: 15131 Cov.: 23

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.540

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.447 AC: 65689 AN: 147014 Hom.: 15132 Cov.: 23 AF XY: 0.453 AC XY: 32303 AN XY: 71244

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.453

Alfa AF: 0.442 Hom.: 1841

Bravo AF: 0.432

Asia WGS AF: 0.559 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs925949; hg19: chr2-222472827;