rs7228984

Variant names:

• chr18-78057704-T-C
• rs7228984

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 0.232 in 152,050 control chromosomes in the GnomAD database, including 4,315 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 0.23 (4315 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 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: 0.232 AC: 35249 AN: 151932 Hom.: 4309 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.232 AC: 35277 AN: 152050 Hom.: 4315 Cov.: 32 AF XY: 0.233 AC XY: 17284 AN XY: 74330

African (AFR) AF: 0.290 AC: 12024 AN: 41472

American (AMR) AF: 0.212 AC: 3240 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1016 AN: 3468

East Asian (EAS) AF: 0.305 AC: 1576 AN: 5164

South Asian (SAS) AF: 0.282 AC: 1356 AN: 4808

European-Finnish (FIN) AF: 0.211 AC: 2231 AN: 10588

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13090 AN: 67958

Other (OTH) AF: 0.232 AC: 489 AN: 2112

Alfa AF: 0.208 Hom.: 9058

Bravo AF: 0.235

Asia WGS AF: 0.262 AC: 910 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	2.6
DANN	Benign	0.64
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs7228984; hg19: chr18-75817704;