rs2207362

Positions:

• chr22-27517426-G-A
• chr22-27517426-G-C
• chr22-27517426-G-T

Variant summary

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

The XR_938124.2(LOC105372981):​n.136-8481C>T 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 0.348 in 151,944 control chromosomes in the GnomAD database, including 9,991 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 (9991 hom., cov: 31)
• Consequence: LOC105372981 XR_938124.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40

Genes affected

LOC105372981 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372981	XR_938124.2	n.136-8481C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52902 AN: 151824 Hom.: 9982 Cov.: 31

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.348 AC: 52949 AN: 151944 Hom.: 9991 Cov.: 31 AF XY: 0.352 AC XY: 26180 AN XY: 74314

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.773

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.363

Alfa AF: 0.306 Hom.: 8791

Bravo AF: 0.352

Asia WGS AF: 0.607 AC: 2108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0040
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2207362; hg19: chr22-27913387;