rs9332436

Positions:

• chr8-48696059-G-A

Variant summary

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

The NR_105002.1(LOC101929268):​n.420-499G>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 0.567 in 152,156 control chromosomes in the GnomAD database, including 28,668 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 0.57 (28668 hom., cov: 33)
• Consequence: LOC101929268 NR_105002.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.525

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929268	NR_105002.1	n.420-499G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000522575.1	n.420-499G>A		intron_variant, non_coding_transcript_variant		2
	ENST00000654201.1	n.271G>A		non_coding_transcript_exon_variant	4/5
	ENST00000657307.1	n.88-499G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86260 AN: 152038 Hom.: 28675 Cov.: 33

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.567 AC: 86272 AN: 152156 Hom.: 28668 Cov.: 33 AF XY: 0.574 AC XY: 42682 AN XY: 74380

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.810

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.588

Alfa AF: 0.632 Hom.: 4125

Bravo AF: 0.537

Asia WGS AF: 0.569 AC: 1977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.7
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332436; hg19: chr8-49608618;