rs497150

Positions:

• chr22-27321755-A-G
• chr22-27321755-A-T

Variant summary

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

The XR_938121.2(LOC105372979):​n.348T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,090 control chromosomes in the GnomAD database, including 10,260 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 0.35 (10260 hom., cov: 32)
• Consequence: LOC105372979 XR_938121.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53

Genes affected

LOC105372979 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372979	XR_938121.2	n.348T>C		non_coding_transcript_exon_variant	2/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52506 AN: 151972 Hom.: 10233 Cov.: 32

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.346 AC: 52595 AN: 152090 Hom.: 10260 Cov.: 32 AF XY: 0.343 AC XY: 25532 AN XY: 74370

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.339

Alfa AF: 0.249 Hom.: 2367

Bravo AF: 0.359

Asia WGS AF: 0.395 AC: 1376 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	0.010
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs497150; hg19: chr22-27717716;