chr22-35235551-C-T

Position:

• chr22-35235551-C-T

Variant summary

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

The XR_938210.3(LOC105373017):​n.3498-2660G>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 0.0744 in 152,140 control chromosomes in the GnomAD database, including 586 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 0.074 (586 hom., cov: 31)
• Consequence: LOC105373017 XR_938210.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

Genes affected

LOC105373017 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373017	XR_938210.3	n.3498-2660G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0744 AC: 11315 AN: 152022 Hom.: 588 Cov.: 31

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0665

Gnomad ASJ AF: 0.0354

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.0488

Gnomad FIN AF: 0.0251

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0414

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0744 AC: 11323 AN: 152140 Hom.: 586 Cov.: 31 AF XY: 0.0734 AC XY: 5460 AN XY: 74388

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.0663

Gnomad4 ASJ AF: 0.0354

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.0486

Gnomad4 FIN AF: 0.0251

Gnomad4 NFE AF: 0.0414

Gnomad4 OTH AF: 0.0568

Alfa AF: 0.0454 Hom.: 274

Bravo AF: 0.0789

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2092331; hg19: chr22-35631544;