chr22-19750087-T-C

Variant names:

• chr22-19750087-T-C
• rs7291533

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 0.3 in 152,074 control chromosomes in the GnomAD database, including 8,205 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 0.30 (8205 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.425 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: 0.300 AC: 45591 AN: 151956 Hom.: 8199 Cov.: 33

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.300 AC: 45604 AN: 152074 Hom.: 8205 Cov.: 33 AF XY: 0.299 AC XY: 22215 AN XY: 74322

African (AFR) AF: 0.112 AC: 4643 AN: 41482

American (AMR) AF: 0.361 AC: 5521 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1194 AN: 3472

East Asian (EAS) AF: 0.129 AC: 667 AN: 5168

South Asian (SAS) AF: 0.440 AC: 2121 AN: 4816

European-Finnish (FIN) AF: 0.341 AC: 3610 AN: 10590

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26909 AN: 67942

Other (OTH) AF: 0.312 AC: 659 AN: 2110

Alfa AF: 0.371 Hom.: 14158

Bravo AF: 0.290

Asia WGS AF: 0.274 AC: 950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.7
DANN	Benign	0.61
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs7291533; hg19: chr22-19737610; COSMIC: COSV60107264;