rs135745

Variant names:

• chr22-38287631-G-C
• rs135745

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 0.474 in 152,030 control chromosomes in the GnomAD database, including 17,581 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 0.47 (17581 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.525 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: 0.474 AC: 71946 AN: 151912 Hom.: 17569 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.474 AC: 71997 AN: 152030 Hom.: 17581 Cov.: 32 AF XY: 0.475 AC XY: 35309 AN XY: 74304

African (AFR) AF: 0.399 AC: 16546 AN: 41478

American (AMR) AF: 0.535 AC: 8169 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1858 AN: 3468

East Asian (EAS) AF: 0.164 AC: 850 AN: 5176

South Asian (SAS) AF: 0.465 AC: 2242 AN: 4818

European-Finnish (FIN) AF: 0.528 AC: 5579 AN: 10558

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35119 AN: 67950

Other (OTH) AF: 0.471 AC: 993 AN: 2108

Alfa AF: 0.504 Hom.: 2448

Bravo AF: 0.471

Asia WGS AF: 0.330 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.64
PhyloP100		-0.083

Splicing

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

Other links and lift over

dbSNP: rs135745; hg19: chr22-38683637;