chr1-116721168-T-C

Variant names:

• chr1-116721168-T-C
• rs624988

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 0.558 in 151,978 control chromosomes in the GnomAD database, including 23,916 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 0.56 (23916 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• Publications: 37 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.597 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: 0.559 AC: 84841 AN: 151860 Hom.: 23909 Cov.: 31

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.558 AC: 84859 AN: 151978 Hom.: 23916 Cov.: 31 AF XY: 0.558 AC XY: 41454 AN XY: 74274

African (AFR) AF: 0.478 AC: 19796 AN: 41422

American (AMR) AF: 0.527 AC: 8047 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2203 AN: 3464

East Asian (EAS) AF: 0.569 AC: 2934 AN: 5156

South Asian (SAS) AF: 0.502 AC: 2418 AN: 4816

European-Finnish (FIN) AF: 0.639 AC: 6763 AN: 10576

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.602 AC: 40890 AN: 67956

Other (OTH) AF: 0.567 AC: 1198 AN: 2112

Alfa AF: 0.584 Hom.: 113118

Bravo AF: 0.544

Asia WGS AF: 0.536 AC: 1863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.22
DANN	Benign	0.74
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs624988; hg19: chr1-117263790; COSMIC: COSV59991330;