chr9-121408212-C-A

Variant names:

• chr9-121408212-C-A
• rs2196311
• ENST00000440807.1:n.86-32164C>A

Variant summary

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

The ENST00000440807.1(ENSG00000227355):​n.86-32164C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 151,908 control chromosomes in the GnomAD database, including 43,300 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 0.74 (43300 hom., cov: 31)
• Consequence: ENSG00000227355 ENST00000440807.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 5 publications found

Genes affected

ENSG00000227355 (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 (NFE) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723324	NR_187153.1	n.404+32887C>A		intron_variant	Intron 2 of 3
LOC102723324	NR_187154.1	n.207+32887C>A		intron_variant	Intron 2 of 3
LOC102723324	NR_187158.1	n.169+32887C>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227355	ENST00000440807.1	n.86-32164C>A		intron_variant	Intron 1 of 2	3
ENSG00000227355	ENST00000635872.1	n.156+32887C>A		intron_variant	Intron 2 of 3	3
ENSG00000227355	ENST00000658975.2	n.170-32164C>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112211 AN: 151790 Hom.: 43301 Cov.: 31

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.739 AC: 112235 AN: 151908 Hom.: 43300 Cov.: 31 AF XY: 0.738 AC XY: 54808 AN XY: 74248

African (AFR) AF: 0.514 AC: 21279 AN: 41386

American (AMR) AF: 0.699 AC: 10668 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2681 AN: 3466

East Asian (EAS) AF: 0.596 AC: 3078 AN: 5162

South Asian (SAS) AF: 0.783 AC: 3760 AN: 4802

European-Finnish (FIN) AF: 0.876 AC: 9255 AN: 10562

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.867 AC: 58902 AN: 67958

Other (OTH) AF: 0.744 AC: 1567 AN: 2106

Alfa AF: 0.819 Hom.: 77851

Bravo AF: 0.716

Asia WGS AF: 0.677 AC: 2357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.65
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs2196311; hg19: chr9-124170490;