rs2122339

chr4-27692567-T-Achr4-27692567-T-C

Variant summary

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

The XR_925517.2(LOC105374548):n.146-2220T>A 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 0.0241 in 152,086 control chromosomes in the GnomAD database, including 139 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 0.024 (139 hom., cov: 33)
• Consequence: LOC105374548 XR_925517.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

Genes affected

LOC105374548 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374548	XR_925517.2	n.146-2220T>A		intron_variant, non_coding_transcript_variant
LOC105374548	XR_925518.2	n.146-2220T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0241 AC: 3658 AN: 151968 Hom.: 136 Cov.: 33

Gnomad AFR AF: 0.0160

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0755

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.0256

Gnomad FIN AF: 0.0286

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00922

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0241 AC: 3668 AN: 152086 Hom.: 139 Cov.: 33 AF XY: 0.0270 AC XY: 2006 AN XY: 74332

Gnomad4 AFR AF: 0.0160

Gnomad4 AMR AF: 0.0761

Gnomad4 ASJ AF: 0.00548

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.0254

Gnomad4 FIN AF: 0.0286

Gnomad4 NFE AF: 0.00922

Gnomad4 OTH AF: 0.0284

Alfa AF: 0.00512 Hom.: 1

Bravo AF: 0.0287

Asia WGS AF: 0.0660 AC: 230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	3.6
Dann	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2122339; hg19: chr4-27694189;