chr1-40779682-C-T

Variant names:

• chr1-40779682-C-T
• rs2769255

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 0.397 in 151,976 control chromosomes in the GnomAD database, including 12,086 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 0.40 (12086 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 8 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 (SAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60220 AN: 151858 Hom.: 12074 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.397 AC: 60263 AN: 151976 Hom.: 12086 Cov.: 31 AF XY: 0.400 AC XY: 29690 AN XY: 74264

African (AFR) AF: 0.382 AC: 15843 AN: 41430

American (AMR) AF: 0.476 AC: 7270 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1358 AN: 3468

East Asian (EAS) AF: 0.467 AC: 2399 AN: 5134

South Asian (SAS) AF: 0.531 AC: 2565 AN: 4826

European-Finnish (FIN) AF: 0.369 AC: 3898 AN: 10576

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25480 AN: 67942

Other (OTH) AF: 0.411 AC: 867 AN: 2110

Alfa AF: 0.376 Hom.: 24595

Bravo AF: 0.398

Asia WGS AF: 0.516 AC: 1794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.69
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2769255; hg19: chr1-41245354;