9-6049547-A-G

Variant names:

• chr9-6049547-A-G
• rs10975412
• ENST00000437881.1:n.149+2039A>G

Variant summary

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

The ENST00000437881.1(ENSG00000228739):​n.149+2039A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,120 control chromosomes in the GnomAD database, including 2,560 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 0.18 (2560 hom., cov: 32)
• Consequence: ENSG00000228739 ENST00000437881.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.692
• Publications: 6 publications found

Genes affected

ENSG00000228739 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000437881.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228739	ENST00000437881.1	TSL:2	n.149+2039A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27308 AN: 152002 Hom.: 2554 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.0204

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.180 AC: 27327 AN: 152120 Hom.: 2560 Cov.: 32 AF XY: 0.179 AC XY: 13327 AN XY: 74342

African (AFR) AF: 0.172 AC: 7151 AN: 41480

American (AMR) AF: 0.163 AC: 2498 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 849 AN: 3472

East Asian (EAS) AF: 0.0204 AC: 106 AN: 5190

South Asian (SAS) AF: 0.229 AC: 1102 AN: 4822

European-Finnish (FIN) AF: 0.172 AC: 1823 AN: 10588

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13114 AN: 67966

Other (OTH) AF: 0.209 AC: 442 AN: 2112

Alfa AF: 0.184 Hom.: 3528

Bravo AF: 0.175

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.2
DANN	Benign	0.70
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs10975412; hg19: chr9-6049547;