chrX-149456568-T-C

Variant names:

• chrX-149456568-T-C
• rs985081
• ENST00000836698.1:n.98-1143T>C

Variant summary

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

The ENST00000836698.1(ENSG00000308827):​n.98-1143T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 111,371 control chromosomes in the GnomAD database, including 1,069 homozygotes. There are 4,547 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 0.14 (1069 hom., 4547 hem., cov: 23)
• Consequence: ENSG00000308827 ENST00000836698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 3 publications found

Genes affected

ENSG00000308827 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836698.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308827	ENST00000836698.1		n.98-1143T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.145 AC: 16095 AN: 111313 Hom.: 1068 Cov.: 23

Gnomad AFR AF: 0.0666

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.00867

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.145 AC: 16101 AN: 111371 Hom.: 1069 Cov.: 23 AF XY: 0.135 AC XY: 4547 AN XY: 33565

African (AFR) AF: 0.0666 AC: 2043 AN: 30692

American (AMR) AF: 0.110 AC: 1163 AN: 10536

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 669 AN: 2647

East Asian (EAS) AF: 0.00869 AC: 31 AN: 3567

South Asian (SAS) AF: 0.130 AC: 345 AN: 2647

European-Finnish (FIN) AF: 0.147 AC: 871 AN: 5924

Middle Eastern (MID) AF: 0.218 AC: 47 AN: 216

European-Non Finnish (NFE) AF: 0.199 AC: 10529 AN: 52942

Other (OTH) AF: 0.146 AC: 223 AN: 1526

Alfa AF: 0.178 Hom.: 11605

Bravo AF: 0.137

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.76
PhyloP100		0.0050

Splicing

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

Other links and lift over

dbSNP: rs985081; hg19: chrX-148538099;