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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.966

Gnomad4 AMR AF: 0.847

Gnomad4 ASJ AF: 0.928

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.923

Gnomad4 FIN AF: 0.855

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.884

Alfa AF: 0.855 Hom.: 79175

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6728440; hg19: chr2-19999346;