rs1020344

chr8-96445305-G-A

Variant summary

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

The XR_928432.2(LOC105375653):n.370-11984G>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 0.233 in 152,126 control chromosomes in the GnomAD database, including 7,536 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 0.23 (7536 hom., cov: 33)
• Consequence: LOC105375653 XR_928432.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

Genes affected

LOC105375653 (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 (AFR) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375653	XR_928432.2	n.370-11984G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35396 AN: 152008 Hom.: 7503 Cov.: 33

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.0882

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.233 AC: 35479 AN: 152126 Hom.: 7536 Cov.: 33 AF XY: 0.233 AC XY: 17345 AN XY: 74374

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.0882

Gnomad4 OTH AF: 0.194

Alfa AF: 0.112 Hom.: 2240

Bravo AF: 0.243

Asia WGS AF: 0.199 AC: 691 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	1.1
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1020344; hg19: chr8-97457533;