2-221936980-C-T

Variant names:

• chr2-221936980-C-T
• rs824931
• XR_923944.3:n.195+23685G>A

Variant summary

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

The XR_923944.3(LOC105373900):​n.195+23685G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 152,054 control chromosomes in the GnomAD database, including 24,153 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 0.53 (24153 hom., cov: 33)
• Consequence: LOC105373900 XR_923944.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.788

Genes affected

LOC105373900 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373900	XR_923944.3	n.195+23685G>A		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80211 AN: 151936 Hom.: 24149 Cov.: 33

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.528 AC: 80234 AN: 152054 Hom.: 24153 Cov.: 33 AF XY: 0.536 AC XY: 39856 AN XY: 74324

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.682

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.643

Gnomad4 OTH AF: 0.558

Alfa AF: 0.634 Hom.: 44856

Bravo AF: 0.505

Asia WGS AF: 0.663 AC: 2303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs824931; hg19: chr2-222801699;