rs885988

Variant names:

• chr22-19743069-G-A
• rs885988

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;