rs7887670

Variant names:

• chrX-34555938-T-C
• rs7887670

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0114 in 112,307 control chromosomes in the GnomAD database, including 22 homozygotes. There are 335 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 0.011 (22 hom., 335 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0114 (1280/112307) while in subpopulation AFR AF = 0.0386 (1195/30949). AF 95% confidence interval is 0.0368. There are 22 homozygotes in GnomAd4. There are 335 alleles in the male GnomAd4 subpopulation. Median coverage is 23. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 22 gene

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: 0.0113 AC: 1274 AN: 112251 Hom.: 22 Cov.: 23

Gnomad AFR AF: 0.0385

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00490

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000373

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00840

Gnomad NFE AF: 0.000338

Gnomad OTH AF: 0.00798

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

GnomAD4 genome AF: 0.0114 AC: 1280 AN: 112307 Hom.: 22 Cov.: 23 AF XY: 0.00971 AC XY: 335 AN XY: 34493

African (AFR) AF: 0.0386 AC: 1195 AN: 30949

American (AMR) AF: 0.00490 AC: 52 AN: 10622

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2647

East Asian (EAS) AF: 0.00 AC: 0 AN: 3555

South Asian (SAS) AF: 0.000374 AC: 1 AN: 2673

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6191

Middle Eastern (MID) AF: 0.00917 AC: 2 AN: 218

European-Non Finnish (NFE) AF: 0.000338 AC: 18 AN: 53245

Other (OTH) AF: 0.00788 AC: 12 AN: 1522

Alfa AF: 0.00892 Hom.: 22

Bravo AF: 0.0133

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.72
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs7887670; hg19: chrX-34574055;