rs9772321

Positions:

• chr8-12634130-T-C

Variant summary

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

The NR_047662.2(LOC729732):​n.1034+25000A>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 0.235 in 149,712 control chromosomes in the GnomAD database, including 4,883 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 0.24 (4883 hom., cov: 31)
• Consequence: LOC729732 NR_047662.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC729732	NR_047662.2	n.1034+25000A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000637678.1	n.937+25000A>G		intron_variant, non_coding_transcript_variant		1
	ENST00000635775.1	n.1011+25000A>G		intron_variant, non_coding_transcript_variant		2
	ENST00000636990.1	n.523-7560A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35220 AN: 149596 Hom.: 4876 Cov.: 31

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.0541

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.235 AC: 35238 AN: 149712 Hom.: 4883 Cov.: 31 AF XY: 0.231 AC XY: 16881 AN XY: 73192

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.0538

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.236

Alfa AF: 0.263 Hom.: 918

Asia WGS AF: 0.124 AC: 432 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9772321; hg19: chr8-12491639;