rs9653202

Variant names:

• chr2-127109531-T-C
• rs9653202
• XR_923311.4:n.671+1716T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_923311.4(LOC105373605):​n.671+1716T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.650
• Publications: 4 publications found

Genes affected

LOC105373605 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105373605	XR_923311.4	n.671+1716T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.156 AC: 6473 AN: 41534

American (AMR) AF: 0.0610 AC: 933 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0813 AC: 282 AN: 3470

East Asian (EAS) AF: 0.0606 AC: 314 AN: 5184

South Asian (SAS) AF: 0.0888 AC: 428 AN: 4822

European-Finnish (FIN) AF: 0.0288 AC: 306 AN: 10610

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0566 AC: 3847 AN: 68020

Other (OTH) AF: 0.0829 AC: 175 AN: 2112

Alfa AF: 0.0748 Hom.: 81

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
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs9653202; hg19: chr2-127867107;