rs7268800

Variant names:

• chr20-39952096-A-G
• rs7268800

Your query was ambiguous. Multiple possible variants found:

• chr20-39952096-A-G
• chr20-39952096-A-T

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 0.262 in 152,058 control chromosomes in the GnomAD database, including 6,202 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 0.26 (6202 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 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: 0.263 AC: 39889 AN: 151940 Hom.: 6200 Cov.: 31

Gnomad AFR AF: 0.0863

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.262 AC: 39896 AN: 152058 Hom.: 6202 Cov.: 31 AF XY: 0.266 AC XY: 19774 AN XY: 74292

African (AFR) AF: 0.0863 AC: 3582 AN: 41516

American (AMR) AF: 0.279 AC: 4266 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 876 AN: 3472

East Asian (EAS) AF: 0.309 AC: 1585 AN: 5128

South Asian (SAS) AF: 0.239 AC: 1155 AN: 4826

European-Finnish (FIN) AF: 0.393 AC: 4152 AN: 10558

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23331 AN: 67962

Other (OTH) AF: 0.261 AC: 549 AN: 2104

Alfa AF: 0.304 Hom.: 9117

Bravo AF: 0.247

Asia WGS AF: 0.252 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.0
DANN	Benign	0.54
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs7268800; hg19: chr20-38580738;