rs9837561

Variant names:

• chr3-3608555-A-C
• rs9837561
• ENST00000420000.6:n.200+18189T>G

Variant summary

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

The ENST00000420000.6(ENSG00000223727):​n.200+18189T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,122 control chromosomes in the GnomAD database, including 2,240 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 0.14 (2240 hom., cov: 32)
• Consequence: ENSG00000223727 ENST00000420000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 2 publications found

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420000.6. 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
	ENSG00000223727	ENST00000420000.6	TSL:4	n.200+18189T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20576 AN: 152006 Hom.: 2242 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0824

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.00424

Gnomad SAS AF: 0.0458

Gnomad FIN AF: 0.0307

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0777

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.135 AC: 20600 AN: 152122 Hom.: 2240 Cov.: 32 AF XY: 0.130 AC XY: 9635 AN XY: 74380

African (AFR) AF: 0.306 AC: 12665 AN: 41430

American (AMR) AF: 0.0823 AC: 1258 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 453 AN: 3472

East Asian (EAS) AF: 0.00425 AC: 22 AN: 5180

South Asian (SAS) AF: 0.0459 AC: 221 AN: 4820

European-Finnish (FIN) AF: 0.0307 AC: 326 AN: 10608

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0777 AC: 5286 AN: 68008

Other (OTH) AF: 0.130 AC: 274 AN: 2112

Alfa AF: 0.109 Hom.: 2202

Bravo AF: 0.148

Asia WGS AF: 0.0460 AC: 162 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.14
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs9837561; hg19: chr3-3650239;