rs641525

chr8-2882980-T-G

Variant summary

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

The NR_168443.1(LOC105377785):n.1171+45216T>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 0.169 in 152,170 control chromosomes in the GnomAD database, including 3,873 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 0.17 (3873 hom., cov: 32)
• Consequence: LOC105377785 NR_168443.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377

Genes affected

LOC105377785 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377785	NR_168443.1	n.1171+45216T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25700 AN: 152052 Hom.: 3871 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.0302

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0570

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.169 AC: 25744 AN: 152170 Hom.: 3873 Cov.: 32 AF XY: 0.168 AC XY: 12533 AN XY: 74428

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.0865

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.0302

Gnomad4 NFE AF: 0.0571

Gnomad4 OTH AF: 0.176

Alfa AF: 0.0809 Hom.: 1443

Bravo AF: 0.185

Asia WGS AF: 0.296 AC: 1030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	3.1
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: rs641525; hg19: chr8-2740502;