chr18-75075090-A-G

Variant names:

• chr18-75075090-A-G
• rs17056274

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 0.0432 in 152,138 control chromosomes in the GnomAD database, including 265 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 0.043 (265 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.982
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 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: 0.0430 AC: 6536 AN: 152020 Hom.: 261 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0189

Gnomad ASJ AF: 0.0441

Gnomad EAS AF: 0.0158

Gnomad SAS AF: 0.0565

Gnomad FIN AF: 0.0221

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0432 AC: 6565 AN: 152138 Hom.: 265 Cov.: 32 AF XY: 0.0431 AC XY: 3208 AN XY: 74376

African (AFR) AF: 0.108 AC: 4473 AN: 41498

American (AMR) AF: 0.0189 AC: 289 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0441 AC: 153 AN: 3472

East Asian (EAS) AF: 0.0159 AC: 82 AN: 5168

South Asian (SAS) AF: 0.0576 AC: 277 AN: 4812

European-Finnish (FIN) AF: 0.0221 AC: 234 AN: 10610

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0141 AC: 955 AN: 67970

Other (OTH) AF: 0.0412 AC: 87 AN: 2112

Alfa AF: 0.0234 Hom.: 265

Bravo AF: 0.0446

Asia WGS AF: 0.0430 AC: 149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.36
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs17056274; hg19: chr18-72787046;