rs7227757

Variant names:

• chr18-2641036-C-T
• rs7227757

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 0.548 in 151,950 control chromosomes in the GnomAD database, including 23,776 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 0.55 (23776 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.713 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: 0.548 AC: 83200 AN: 151832 Hom.: 23741 Cov.: 31

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.548 AC: 83299 AN: 151950 Hom.: 23776 Cov.: 31 AF XY: 0.545 AC XY: 40485 AN XY: 74266

African (AFR) AF: 0.720 AC: 29834 AN: 41440

American (AMR) AF: 0.542 AC: 8276 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1524 AN: 3466

East Asian (EAS) AF: 0.372 AC: 1922 AN: 5162

South Asian (SAS) AF: 0.459 AC: 2215 AN: 4824

European-Finnish (FIN) AF: 0.475 AC: 4997 AN: 10524

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32932 AN: 67944

Other (OTH) AF: 0.538 AC: 1136 AN: 2110

Alfa AF: 0.501 Hom.: 26922

Bravo AF: 0.567

Asia WGS AF: 0.432 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.53
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs7227757; hg19: chr18-2641035;