22-35396981-T-C

Variant names:

• chr22-35396981-T-C
• rs743811

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 0.258 in 151,942 control chromosomes in the GnomAD database, including 5,771 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 0.26 (5771 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 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: 0.258 AC: 39158 AN: 151824 Hom.: 5777 Cov.: 31

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.258 AC: 39151 AN: 151942 Hom.: 5771 Cov.: 31 AF XY: 0.268 AC XY: 19876 AN XY: 74266

African (AFR) AF: 0.156 AC: 6471 AN: 41440

American (AMR) AF: 0.309 AC: 4715 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 986 AN: 3460

East Asian (EAS) AF: 0.667 AC: 3429 AN: 5144

South Asian (SAS) AF: 0.411 AC: 1981 AN: 4824

European-Finnish (FIN) AF: 0.312 AC: 3291 AN: 10560

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17431 AN: 67942

Other (OTH) AF: 0.260 AC: 549 AN: 2112

Alfa AF: 0.263 Hom.: 23311

Bravo AF: 0.258

Asia WGS AF: 0.515 AC: 1791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.1
DANN	Benign	0.33
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs743811; hg19: chr22-35792974;