rs3027415

Variant names:

• chrX-43755194-T-C
• rs3027415

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 0.157 in 111,661 control chromosomes in the GnomAD database, including 1,371 homozygotes. There are 5,047 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 0.16 (1371 hom., 5047 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.82
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 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: 0.157 AC: 17557 AN: 111603 Hom.: 1373 Cov.: 23

Gnomad AFR AF: 0.0491

Gnomad AMI AF: 0.0486

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0210

Gnomad SAS AF: 0.0754

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.157 AC: 17549 AN: 111661 Hom.: 1371 Cov.: 23 AF XY: 0.149 AC XY: 5047 AN XY: 33863

African (AFR) AF: 0.0491 AC: 1512 AN: 30816

American (AMR) AF: 0.112 AC: 1189 AN: 10574

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 527 AN: 2643

East Asian (EAS) AF: 0.0205 AC: 73 AN: 3559

South Asian (SAS) AF: 0.0756 AC: 200 AN: 2646

European-Finnish (FIN) AF: 0.194 AC: 1165 AN: 6004

Middle Eastern (MID) AF: 0.293 AC: 63 AN: 215

European-Non Finnish (NFE) AF: 0.236 AC: 12528 AN: 53011

Other (OTH) AF: 0.171 AC: 259 AN: 1514

Alfa AF: 0.211 Hom.: 14536

Bravo AF: 0.149

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	20
DANN	Benign	0.43
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs3027415; hg19: chrX-43614441;