22-16437595-T-C

Position:

• chr22-16437595-T-C

Variant summary

Our verdict is Likely benign. Variant got -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 0.55 (7499 hom., cov: 37)
  • Failed GnomAD Quality Control
• Consequence: SLC9B1P4 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241

Genes affected

SLC9B1P4 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=2.625).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC9B1P4		n.16437595T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC9B1P4	ENST00000421957.1	n.846+692A>G		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.00 AC: 63021 AN: 115134 Hom.: 7484 Cov.: 37 FAILED QC

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.613

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.560

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: 0.547 AC: 63065 AN: 115202 Hom.: 7499 Cov.: 37 AF XY: 0.545 AC XY: 30953 AN XY: 56758

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.565

Alfa AF: 0.382 Hom.: 914

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	2.6

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2027653; hg19: -;