rs2996005

chr1-221323259-T-Cchr1-221323259-T-G

Variant summary

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

The XR_922621.2(LOC105372932):n.454+16283T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,996 control chromosomes in the GnomAD database, including 18,680 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 0.49 (18680 hom., cov: 32)
• Consequence: LOC105372932 XR_922621.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68

Genes affected

LOC105372932 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372932	XR_922621.2	n.454+16283T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74857 AN: 151878 Hom.: 18656 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.493 AC: 74937 AN: 151996 Hom.: 18680 Cov.: 32 AF XY: 0.489 AC XY: 36300 AN XY: 74304

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.506

Alfa AF: 0.516 Hom.: 35471

Bravo AF: 0.490

Asia WGS AF: 0.373 AC: 1295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.27
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2996005; hg19: chr1-221496601; COSMIC: COSV60031435;