rs6623918

Variant names:

• chrX-87161008-G-A
• rs6623918

Your query was ambiguous. Multiple possible variants found:

• chrX-87161008-G-A
• chrX-87161008-G-C
• chrX-87161008-G-T

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 0.068 in 111,096 control chromosomes in the GnomAD database, including 259 homozygotes. There are 2,326 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 0.068 (259 hom., 2326 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.247 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: 0.0681 AC: 7560 AN: 111043 Hom.: 259 Cov.: 22

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0331

Gnomad ASJ AF: 0.0470

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.0284

Gnomad MID AF: 0.0417

Gnomad NFE AF: 0.0373

Gnomad OTH AF: 0.0628

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

GnomAD4 genome AF: 0.0680 AC: 7558 AN: 111096 Hom.: 259 Cov.: 22 AF XY: 0.0697 AC XY: 2326 AN XY: 33356

African (AFR) AF: 0.120 AC: 3665 AN: 30517

American (AMR) AF: 0.0329 AC: 345 AN: 10483

Ashkenazi Jewish (ASJ) AF: 0.0470 AC: 124 AN: 2636

East Asian (EAS) AF: 0.140 AC: 488 AN: 3498

South Asian (SAS) AF: 0.263 AC: 685 AN: 2606

European-Finnish (FIN) AF: 0.0284 AC: 169 AN: 5951

Middle Eastern (MID) AF: 0.0411 AC: 9 AN: 219

European-Non Finnish (NFE) AF: 0.0373 AC: 1975 AN: 52999

Other (OTH) AF: 0.0653 AC: 98 AN: 1501

Alfa AF: 0.0464 Hom.: 256

Bravo AF: 0.0671

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.53
DANN	Benign	0.22
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs6623918; hg19: chrX-86416011;