rs885988

Positions:

• chr22-19743069-G-A
• chr22-19743069-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.605 in 152,036 control chromosomes in the GnomAD database, including 29,022 homozygotes. 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 0.61 (29022 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.823

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91920 AN: 151918 Hom.: 28984 Cov.: 33

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.605 AC: 92016 AN: 152036 Hom.: 29022 Cov.: 33 AF XY: 0.608 AC XY: 45196 AN XY: 74326

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.860

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.592

Alfa AF: 0.524 Hom.: 27550

Bravo AF: 0.623

Asia WGS AF: 0.732 AC: 2544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.28
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs885988; hg19: chr22-19730592;