rs2223605

Variant names:

• chr6-9440022-G-A
• rs2223605

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.33 in 152,002 control chromosomes in the GnomAD database, including 8,615 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 0.33 (8615 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 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: 0.330 AC: 50085 AN: 151884 Hom.: 8599 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.330 AC: 50155 AN: 152002 Hom.: 8615 Cov.: 32 AF XY: 0.329 AC XY: 24424 AN XY: 74316

African (AFR) AF: 0.425 AC: 17620 AN: 41458

American (AMR) AF: 0.296 AC: 4520 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1456 AN: 3472

East Asian (EAS) AF: 0.404 AC: 2088 AN: 5162

South Asian (SAS) AF: 0.312 AC: 1504 AN: 4822

European-Finnish (FIN) AF: 0.201 AC: 2125 AN: 10568

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19825 AN: 67922

Other (OTH) AF: 0.340 AC: 717 AN: 2110

Alfa AF: 0.326 Hom.: 1239

Bravo AF: 0.337

Asia WGS AF: 0.363 AC: 1262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.4
DANN	Benign	0.78
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs2223605; hg19: chr6-9440255;