rs2504785

Positions:

• chr1-27392450-G-A
• chr1-27392450-G-C
• chr1-27392450-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 0.881 in 152,250 control chromosomes in the GnomAD database, including 59,371 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 0.88 (59371 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.881 AC: 134043 AN: 152132 Hom.: 59332 Cov.: 33

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.881 AC: 134135 AN: 152250 Hom.: 59371 Cov.: 33 AF XY: 0.884 AC XY: 65831 AN XY: 74430

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.930

Gnomad4 ASJ AF: 0.900

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.961

Gnomad4 FIN AF: 0.906

Gnomad4 NFE AF: 0.908

Gnomad4 OTH AF: 0.889

Alfa AF: 0.905 Hom.: 2994

Bravo AF: 0.895

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2504785; hg19: chr1-27718954;