22-16437595-T-C

Variant names:

• chr22-16437595-T-C
• rs2027653

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 0.55 (7499 hom., cov: 37)
  • Failed GnomAD Quality Control
• Consequence: SLC9B1P4 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241
• Publications: 1 publications found

Genes affected

SLC9B1P4 (HGNC:43583): (solute carrier family 9 member B1 pseudogene 4)

ACMG classification

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

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421957.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC9B1P4	ENST00000421957.1	TSL:6	n.846+692A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.547 AC: 63021 AN: 115134 Hom.: 7484 Cov.: 37

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

African (AFR) AF: 0.505 AC: 14515 AN: 28768

American (AMR) AF: 0.552 AC: 6712 AN: 12152

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 1636 AN: 2754

East Asian (EAS) AF: 0.567 AC: 2435 AN: 4292

South Asian (SAS) AF: 0.598 AC: 2500 AN: 4180

European-Finnish (FIN) AF: 0.509 AC: 3773 AN: 7418

Middle Eastern (MID) AF: 0.621 AC: 154 AN: 248

European-Non Finnish (NFE) AF: 0.566 AC: 29990 AN: 53006

Other (OTH) AF: 0.565 AC: 930 AN: 1646

Alfa AF: 0.382 Hom.: 914

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	2.6
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs2027653;