rs987710

Positions:

• chr22-22158022-G-A

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 0.612 in 151,904 control chromosomes in the GnomAD database, including 29,439 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 (29439 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92967 AN: 151790 Hom.: 29443 Cov.: 31

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.612 AC: 92978 AN: 151904 Hom.: 29439 Cov.: 31 AF XY: 0.619 AC XY: 45972 AN XY: 74264

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.757

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.618

Alfa AF: 0.650 Hom.: 22092

Bravo AF: 0.600

Asia WGS AF: 0.604 AC: 2096 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.42
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs987710; hg19: chr22-22512415;