rs2853320

chr8-97271295-C-G

Variant summary

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

The NR_125390.1(LOC101927066):n.471+147775G>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 0.172 in 152,048 control chromosomes in the GnomAD database, including 4,111 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 (4111 hom., cov: 32)
• Consequence: LOC101927066 NR_125390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148

Genes affected

LOC101927066 (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 = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927066	NR_125390.1	n.471+147775G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26067 AN: 151930 Hom.: 4109 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0651

Gnomad EAS AF: 0.0882

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0527

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0671

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.172 AC: 26094 AN: 152048 Hom.: 4111 Cov.: 32 AF XY: 0.168 AC XY: 12475 AN XY: 74326

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.0651

Gnomad4 EAS AF: 0.0875

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0527

Gnomad4 NFE AF: 0.0671

Gnomad4 OTH AF: 0.123

Alfa AF: 0.128 Hom.: 319

Bravo AF: 0.188

Asia WGS AF: 0.115 AC: 399 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	1.9
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2853320; hg19: chr8-98283523;