rs9772321

Variant names:

• chr8-12634130-T-C
• rs9772321
• ENST00000637678.1:n.937+25000A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000637678.1(ENSG00000283674):​n.937+25000A>G variant causes a intron 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: ENSG00000283674 ENST00000637678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160
• Publications: 0 publications found

Genes affected

ENSG00000283674 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637678.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC729732	NR_047662.2		n.1034+25000A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283674	ENST00000637678.1	TSL:1	n.937+25000A>G		intron	N/A
	ENSG00000283674	ENST00000635775.1	TSL:2	n.1011+25000A>G		intron	N/A
	ENSG00000283674	ENST00000636990.2	TSL:3	n.523-7560A>G		intron	N/A

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

African (AFR) AF: 0.202 AC: 8007 AN: 39580

American (AMR) AF: 0.271 AC: 4100 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 964 AN: 3446

East Asian (EAS) AF: 0.0538 AC: 277 AN: 5148

South Asian (SAS) AF: 0.162 AC: 775 AN: 4796

European-Finnish (FIN) AF: 0.209 AC: 2200 AN: 10528

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18174 AN: 67812

Other (OTH) AF: 0.236 AC: 493 AN: 2086

Alfa AF: 0.263 Hom.: 918

Asia WGS AF: 0.124 AC: 432 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.51
PhyloP100		-0.16

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9772321;

hg19: chr8-12491639;