rs6630351

Variant names:

• chrX-27086968-A-G
• rs6630351
• ENST00000609836.1:n.90-43848T>C

Your query was ambiguous. Multiple possible variants found:

• chrX-27086968-A-G
• chrX-27086968-A-T

Variant summary

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

The ENST00000609836.1(ENSG00000228933):​n.90-43848T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 110,858 control chromosomes in the GnomAD database, including 4,103 homozygotes. There are 10,062 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 0.30 (4103 hom., 10062 hem., cov: 22)
• Consequence: ENSG00000228933 ENST00000609836.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174

Genes affected

ENSG00000228933 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.526 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
ENSG00000228933	ENST00000609836.1	n.90-43848T>C		intron_variant	Intron 1 of 1	3
ENSG00000228933	ENST00000717233.1	n.1017-43848T>C		intron_variant	Intron 9 of 10
ENSG00000228933	ENST00000717234.1	n.1155-43848T>C		intron_variant	Intron 10 of 11

Frequencies

GnomAD3 genomes AF: 0.304 AC: 33640 AN: 110801 Hom.: 4102 Cov.: 22

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.304 AC: 33663 AN: 110858 Hom.: 4103 Cov.: 22 AF XY: 0.304 AC XY: 10062 AN XY: 33102

African (AFR) AF: 0.160 AC: 4918 AN: 30657

American (AMR) AF: 0.435 AC: 4514 AN: 10384

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 661 AN: 2632

East Asian (EAS) AF: 0.546 AC: 1888 AN: 3456

South Asian (SAS) AF: 0.456 AC: 1194 AN: 2619

European-Finnish (FIN) AF: 0.359 AC: 2083 AN: 5798

Middle Eastern (MID) AF: 0.214 AC: 46 AN: 215

European-Non Finnish (NFE) AF: 0.335 AC: 17697 AN: 52891

Other (OTH) AF: 0.310 AC: 473 AN: 1525

Alfa AF: 0.304 Hom.: 9808

Bravo AF: 0.308

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.67
PhyloP100		-0.17

Splicing

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

Publications

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Other links and lift over

dbSNP: rs6630351; hg19: chrX-27105085;