rs6616402

Variant names:

• chrX-80003347-A-G
• rs6616402

Variant summary

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

The variant allele was found at a frequency of 0.238 in 110,577 control chromosomes in the GnomAD database, including 2,368 homozygotes. There are 7,794 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 0.24 (2368 hom., 7794 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 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

Frequencies

GnomAD3 genomes AF: 0.238 AC: 26272 AN: 110521 Hom.: 2368 Cov.: 23 AF XY: 0.236 AC XY: 7783 AN XY: 33015

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.238 AC: 26281 AN: 110577 Hom.: 2368 Cov.: 23 AF XY: 0.236 AC XY: 7794 AN XY: 33079

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.262

Alfa AF: 0.242 Hom.: 1483

Bravo AF: 0.244

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6616402; hg19: chrX-79258846;