rs497150

Variant names:

• chr22-27321755-A-G
• rs497150
• XR_938121.2:n.348T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

LOC105372979 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105372979	XR_938121.2	n.348T>C		non_coding_transcript_exon_variant	Exon 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302993	ENST00000790894.1	n.582+257T>C		intron_variant	Intron 5 of 5
ENSG00000302993	ENST00000790897.1	n.158+257T>C		intron_variant	Intron 1 of 1
ENSG00000302993	ENST00000790895.1	n.*108T>C		downstream_gene_variant
ENSG00000302993	ENST00000790896.1	n.*226T>C		downstream_gene_variant

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

African (AFR) AF: 0.544 AC: 22536 AN: 41462

American (AMR) AF: 0.303 AC: 4637 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1080 AN: 3470

East Asian (EAS) AF: 0.408 AC: 2104 AN: 5158

South Asian (SAS) AF: 0.329 AC: 1586 AN: 4822

European-Finnish (FIN) AF: 0.250 AC: 2650 AN: 10590

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16974 AN: 67980

Other (OTH) AF: 0.339 AC: 715 AN: 2112

Alfa AF: 0.269 Hom.: 4161

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
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs497150; hg19: chr22-27717716;