rs1041668

Variant names:

• chrX-66866114-G-A
• rs1041668

Your query was ambiguous. Multiple possible variants found:

• chrX-66866114-G-A
• chrX-66866114-G-C
• chrX-66866114-G-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.65 (20514 hom., 21885 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 7 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

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: 0.655 AC: 72394 AN: 110591 Hom.: 20522 Cov.: 23

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.928

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.754

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.707

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.654 AC: 72384 AN: 110644 Hom.: 20514 Cov.: 23 AF XY: 0.665 AC XY: 21885 AN XY: 32892

African (AFR) AF: 0.138 AC: 4232 AN: 30613

American (AMR) AF: 0.832 AC: 8588 AN: 10319

Ashkenazi Jewish (ASJ) AF: 0.928 AC: 2446 AN: 2635

East Asian (EAS) AF: 0.998 AC: 3472 AN: 3479

South Asian (SAS) AF: 0.921 AC: 2379 AN: 2583

European-Finnish (FIN) AF: 0.821 AC: 4766 AN: 5805

Middle Eastern (MID) AF: 0.753 AC: 162 AN: 215

European-Non Finnish (NFE) AF: 0.846 AC: 44669 AN: 52813

Other (OTH) AF: 0.710 AC: 1070 AN: 1507

Alfa AF: 0.795 Hom.: 50237

Bravo AF: 0.637

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.60
DANN	Benign	0.44
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1041668; hg19: chrX-66085956; COSMIC: COSV68315964;