X-9279959-T-G

Variant names:

• chrX-9279959-T-G
• rs1024443
• ENST00000651278.1:c.-355+15678A>C

Variant summary

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

The ENST00000651278.1(FAM9B):​c.-355+15678A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 110,566 control chromosomes in the GnomAD database, including 13,597 homozygotes. There are 18,085 hemizygotes in GnomAD. 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 0.55 (13597 hom., 18085 hem., cov: 23)
• Consequence: FAM9B ENST00000651278.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 0 publications found

Genes affected

FAM9B (HGNC:18404): (family with sequence similarity 9 member B) This gene is a member of a gene family which arose through duplication on the X chromosome. The encoded protein may be localized to the nucleus as the protein contains several nuclear localization signals, and has similarity to a synaptonemal complex protein. [provided by RefSeq, Aug 2011]

ENSG00000302729 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM9B	ENST00000651278.1	c.-355+15678A>C		intron_variant	Intron 1 of 10			ENSP00000498495.1
ENSG00000302729	ENST00000789256.1	n.79-7023A>C		intron_variant	Intron 1 of 1
ENSG00000302729	ENST00000789257.1	n.299-7023A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.550 AC: 60789 AN: 110512 Hom.: 13602 Cov.: 23

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.607

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.550 AC: 60787 AN: 110566 Hom.: 13597 Cov.: 23 AF XY: 0.549 AC XY: 18085 AN XY: 32912

African (AFR) AF: 0.209 AC: 6391 AN: 30550

American (AMR) AF: 0.545 AC: 5670 AN: 10396

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 1766 AN: 2628

East Asian (EAS) AF: 0.782 AC: 2715 AN: 3474

South Asian (SAS) AF: 0.668 AC: 1750 AN: 2619

European-Finnish (FIN) AF: 0.678 AC: 3955 AN: 5836

Middle Eastern (MID) AF: 0.615 AC: 131 AN: 213

European-Non Finnish (NFE) AF: 0.705 AC: 37117 AN: 52677

Other (OTH) AF: 0.571 AC: 859 AN: 1504

Alfa AF: 0.646 Hom.: 91316

Bravo AF: 0.526

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.35
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs1024443; hg19: chrX-9247999;