rs640009

Variant names:

• chrX-112844240-T-C
• rs640009
• ENST00000738665.1:n.165-2727T>C

Variant summary

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

The ENST00000738665.1(ENSG00000286072):​n.165-2727T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 111,578 control chromosomes in the GnomAD database, including 3,999 homozygotes. There are 9,487 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 0.28 (3999 hom., 9487 hem., cov: 24)
• Consequence: ENSG00000286072 ENST00000738665.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316
• Publications: 1 publications found

Genes affected

ENSG00000286072 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985651	XR_001755993.2	n.144-19T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286072	ENST00000738665.1	n.165-2727T>C		intron_variant	Intron 1 of 2
ENSG00000286072	ENST00000738666.1	n.137-19T>C		intron_variant	Intron 1 of 3
ENSG00000286072	ENST00000738667.1	n.151-19T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.285 AC: 31758 AN: 111522 Hom.: 3995 Cov.: 24

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.0532

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.285 AC: 31786 AN: 111578 Hom.: 3999 Cov.: 24 AF XY: 0.281 AC XY: 9487 AN XY: 33794

African (AFR) AF: 0.419 AC: 12839 AN: 30652

American (AMR) AF: 0.442 AC: 4665 AN: 10566

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 299 AN: 2638

East Asian (EAS) AF: 0.580 AC: 2027 AN: 3492

South Asian (SAS) AF: 0.176 AC: 473 AN: 2684

European-Finnish (FIN) AF: 0.266 AC: 1590 AN: 5985

Middle Eastern (MID) AF: 0.196 AC: 42 AN: 214

European-Non Finnish (NFE) AF: 0.176 AC: 9356 AN: 53140

Other (OTH) AF: 0.300 AC: 459 AN: 1530

Alfa AF: 0.223 Hom.: 6792

Bravo AF: 0.312

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.5
DANN	Benign	0.81
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs640009; hg19: chrX-112087468;