9-7918996-A-G

Variant names:

• chr9-7918996-A-G
• rs2224601
• ENST00000668681.1:n.567-4255T>C

Variant summary

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

The ENST00000668681.1(ENSG00000231902):​n.567-4255T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,244 control chromosomes in the GnomAD database, including 52,513 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 0.83 (52513 hom., cov: 33)
• Consequence: ENSG00000231902 ENST00000668681.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619

Genes affected

ENSG00000231902 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375971	XR_929463.3	n.671-4255T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231902	ENST00000668681.1	n.567-4255T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125865 AN: 152126 Hom.: 52464 Cov.: 33

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.827 AC: 125974 AN: 152244 Hom.: 52513 Cov.: 33 AF XY: 0.827 AC XY: 61550 AN XY: 74430

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.707

Gnomad4 EAS AF: 0.963

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.777

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.806

Alfa AF: 0.775 Hom.: 89239

Bravo AF: 0.836

Asia WGS AF: 0.890 AC: 3095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.31
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2224601; hg19: chr9-7918996;