rs4523235

Positions:

• chr8-131225922-A-G

Variant summary

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

The XR_007061183.1(LOC105375760):​n.435-63966A>G 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 0.28 in 152,078 control chromosomes in the GnomAD database, including 6,124 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 0.28 (6124 hom., cov: 32)
• Consequence: LOC105375760 XR_007061183.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

Genes affected

LOC105375760 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375760	XR_007061183.1	n.435-63966A>G		intron_variant, non_coding_transcript_variant
LOC105375760	XR_928653.3	n.297-63966A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42443 AN: 151960 Hom.: 6102 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.280 AC: 42517 AN: 152078 Hom.: 6124 Cov.: 32 AF XY: 0.273 AC XY: 20297 AN XY: 74344

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.255

Alfa AF: 0.281 Hom.: 12752

Bravo AF: 0.278

Asia WGS AF: 0.209 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.1
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4523235; hg19: chr8-132238169;