1-207492716-C-T

Variant names:

• chr1-207492716-C-T
• rs4618971

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 0.762 in 152,072 control chromosomes in the GnomAD database, including 44,433 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 0.76 (44433 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 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: 0.762 AC: 115859 AN: 151954 Hom.: 44421 Cov.: 31

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.762 AC: 115920 AN: 152072 Hom.: 44433 Cov.: 31 AF XY: 0.767 AC XY: 56988 AN XY: 74342

African (AFR) AF: 0.715 AC: 29633 AN: 41424

American (AMR) AF: 0.791 AC: 12092 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2487 AN: 3470

East Asian (EAS) AF: 0.959 AC: 4971 AN: 5182

South Asian (SAS) AF: 0.877 AC: 4228 AN: 4822

European-Finnish (FIN) AF: 0.770 AC: 8150 AN: 10578

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.765 AC: 51982 AN: 67992

Other (OTH) AF: 0.748 AC: 1579 AN: 2112

Alfa AF: 0.765 Hom.: 24114

Bravo AF: 0.762

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.012
DANN	Benign	0.60
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs4618971; hg19: chr1-207666061;