rs6728440

Variant names:

• chr2-19799585-G-A
• rs6728440

Your query was ambiguous. Multiple possible variants found:

• chr2-19799585-G-A
• chr2-19799585-G-C
• chr2-19799585-G-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 0.887 in 152,198 control chromosomes in the GnomAD database, including 60,202 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 0.89 (60202 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.958 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: 0.887 AC: 134949 AN: 152080 Hom.: 60140 Cov.: 31

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.928

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.887 AC: 135068 AN: 152198 Hom.: 60202 Cov.: 31 AF XY: 0.890 AC XY: 66247 AN XY: 74418

African (AFR) AF: 0.966 AC: 40126 AN: 41548

American (AMR) AF: 0.847 AC: 12952 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.928 AC: 3221 AN: 3470

East Asian (EAS) AF: 0.965 AC: 4991 AN: 5174

South Asian (SAS) AF: 0.923 AC: 4448 AN: 4818

European-Finnish (FIN) AF: 0.855 AC: 9053 AN: 10590

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.843 AC: 57311 AN: 67992

Other (OTH) AF: 0.884 AC: 1868 AN: 2114

Alfa AF: 0.860 Hom.: 128330

Bravo AF: 0.886

Asia WGS AF: 0.936 AC: 3254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.096
DANN	Benign	0.46
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6728440; hg19: chr2-19999346;