rs1780746

Variant names:

• chr1-78716876-G-A
• rs1780746

Your query was ambiguous. Multiple possible variants found:

• chr1-78716876-G-A
• chr1-78716876-G-C

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 0.857 in 152,122 control chromosomes in the GnomAD database, including 55,920 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 0.86 (55920 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 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: 0.857 AC: 130240 AN: 152004 Hom.: 55872 Cov.: 32

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.857 AC: 130345 AN: 152122 Hom.: 55920 Cov.: 32 AF XY: 0.858 AC XY: 63804 AN XY: 74358

African (AFR) AF: 0.883 AC: 36671 AN: 41508

American (AMR) AF: 0.876 AC: 13379 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.851 AC: 2955 AN: 3472

East Asian (EAS) AF: 0.975 AC: 5055 AN: 5186

South Asian (SAS) AF: 0.883 AC: 4254 AN: 4820

European-Finnish (FIN) AF: 0.844 AC: 8930 AN: 10580

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.830 AC: 56419 AN: 67980

Other (OTH) AF: 0.869 AC: 1834 AN: 2110

Alfa AF: 0.842 Hom.: 221382

Bravo AF: 0.861

Asia WGS AF: 0.935 AC: 3251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.79
PhyloP100		-0.0030

Splicing

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

Other links and lift over

dbSNP: rs1780746; hg19: chr1-79182561;