rs9653202

chr2-127109531-T-C

Variant summary

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

The XR_923311.4(LOC105373605):n.671+1716T>C 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 0.0843 in 152,252 control chromosomes in the GnomAD database, including 722 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 0.084 (722 hom., cov: 33)
• Consequence: LOC105373605 XR_923311.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.650

Genes affected

LOC105373605 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373605	XR_923311.4	n.671+1716T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0840 AC: 12785 AN: 152134 Hom.: 714 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0429

Gnomad AMR AF: 0.0611

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.0602

Gnomad SAS AF: 0.0885

Gnomad FIN AF: 0.0288

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0566

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.0843 AC: 12828 AN: 152252 Hom.: 722 Cov.: 33 AF XY: 0.0836 AC XY: 6224 AN XY: 74450

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.0610

Gnomad4 ASJ AF: 0.0813

Gnomad4 EAS AF: 0.0606

Gnomad4 SAS AF: 0.0888

Gnomad4 FIN AF: 0.0288

Gnomad4 NFE AF: 0.0566

Gnomad4 OTH AF: 0.0829

Alfa AF: 0.0723 Hom.: 69

Bravo AF: 0.0884

Asia WGS AF: 0.103 AC: 357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	17
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9653202; hg19: chr2-127867107;