rs16394

chr22-38896462-T-TCATA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000656940.1(ENSG00000288106):n.172-4583_172-4582insTACA variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.70 (38978 hom., cov: 0)
• Consequence: ENST00000656940.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373032	XR_938256.2	n.721+9457_721+9458insTACA		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656940.1	n.172-4583_172-4582insTACA		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.704 AC: 105792 AN: 150274 Hom.: 38936 Cov.: 0

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.704 AC: 105875 AN: 150378 Hom.: 38978 Cov.: 0 AF XY: 0.701 AC XY: 51358 AN XY: 73310

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.841

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.676

Alfa AF: 0.481 Hom.: 805

Asia WGS AF: 0.745 AC: 2575 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16394; hg19: chr22-39292467;