rs2357569

Positions:

• chr8-66004902-A-G

Variant summary

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

The XR_929008.3(LOC105375883):​n.431-5935T>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 0.469 in 152,122 control chromosomes in the GnomAD database, including 21,542 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 0.47 (21542 hom., cov: 32)
• Consequence: LOC105375883 XR_929008.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483

Genes affected

LOC105375883 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375883	XR_929008.3	n.431-5935T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71300 AN: 152002 Hom.: 21491 Cov.: 32

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.469 AC: 71408 AN: 152122 Hom.: 21542 Cov.: 32 AF XY: 0.460 AC XY: 34248 AN XY: 74400

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.460

Alfa AF: 0.404 Hom.: 1976

Bravo AF: 0.494

Asia WGS AF: 0.247 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2357569; hg19: chr8-66917137;