rs6641116

Variant names:

• chrX-12828116-A-T
• rs6641116

Variant summary

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

The variant allele was found at a frequency of 0.309 in 110,826 control chromosomes in the GnomAD database, including 4,198 homozygotes. There are 10,257 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 0.31 (4198 hom., 10257 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 3 publications found

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 = 0.52 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: 0.310 AC: 34299 AN: 110770 Hom.: 4204 Cov.: 22

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.309 AC: 34298 AN: 110826 Hom.: 4198 Cov.: 22 AF XY: 0.310 AC XY: 10257 AN XY: 33084

African (AFR) AF: 0.146 AC: 4479 AN: 30584

American (AMR) AF: 0.379 AC: 3979 AN: 10501

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 807 AN: 2623

East Asian (EAS) AF: 0.540 AC: 1886 AN: 3493

South Asian (SAS) AF: 0.375 AC: 963 AN: 2568

European-Finnish (FIN) AF: 0.368 AC: 2159 AN: 5862

Middle Eastern (MID) AF: 0.362 AC: 77 AN: 213

European-Non Finnish (NFE) AF: 0.363 AC: 19193 AN: 52814

Other (OTH) AF: 0.317 AC: 474 AN: 1497

Alfa AF: 0.334 Hom.: 2195

Bravo AF: 0.305

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.83
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs6641116; hg19: chrX-12846235;