rs2568112

chr2-81764978-G-Achr2-81764978-G-T

Variant summary

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

The XR_007088668.1(LOC102724542):n.668-83775G>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 0.361 in 152,008 control chromosomes in the GnomAD database, including 10,562 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 0.36 (10562 hom., cov: 32)
• Consequence: LOC102724542 XR_007088668.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.933

Genes affected

LOC102724542 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724542	XR_007088668.1	n.668-83775G>A		intron_variant, non_coding_transcript_variant
LOC102724542	XR_940294.2	n.576-83775G>A		intron_variant, non_coding_transcript_variant
LOC102724542	XR_940295.2	n.498-83775G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54930 AN: 151890 Hom.: 10559 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.361 AC: 54948 AN: 152008 Hom.: 10562 Cov.: 32 AF XY: 0.363 AC XY: 26997 AN XY: 74286

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.334

Alfa AF: 0.404 Hom.: 5985

Bravo AF: 0.338

Asia WGS AF: 0.263 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.60
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2568112; hg19: chr2-81992102;