rs1468772

Variant names:

• chr1-156146697-T-G
• rs1468772

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 0.218 in 152,138 control chromosomes in the GnomAD database, including 4,600 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 0.22 (4600 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.284 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: 0.218 AC: 33182 AN: 152020 Hom.: 4594 Cov.: 32

Gnomad AFR AF: 0.0526

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.218 AC: 33195 AN: 152138 Hom.: 4600 Cov.: 32 AF XY: 0.222 AC XY: 16490 AN XY: 74372

African (AFR) AF: 0.0524 AC: 2178 AN: 41530

American (AMR) AF: 0.291 AC: 4455 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 838 AN: 3472

East Asian (EAS) AF: 0.193 AC: 997 AN: 5170

South Asian (SAS) AF: 0.291 AC: 1402 AN: 4820

European-Finnish (FIN) AF: 0.316 AC: 3344 AN: 10588

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19191 AN: 67956

Other (OTH) AF: 0.248 AC: 523 AN: 2112

Alfa AF: 0.265 Hom.: 12032

Bravo AF: 0.212

Asia WGS AF: 0.267 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.5
DANN	Benign	0.37
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs1468772; hg19: chr1-156116488;