1-149920979-A-G

Variant names:

• chr1-149920979-A-G
• rs11205277

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 0.315 in 152,136 control chromosomes in the GnomAD database, including 9,026 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 0.32 (9026 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480
• Publications: 76 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.432 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: 0.316 AC: 47973 AN: 152018 Hom.: 9029 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.315 AC: 47967 AN: 152136 Hom.: 9026 Cov.: 32 AF XY: 0.309 AC XY: 22998 AN XY: 74380

African (AFR) AF: 0.112 AC: 4656 AN: 41538

American (AMR) AF: 0.308 AC: 4713 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1008 AN: 3472

East Asian (EAS) AF: 0.311 AC: 1610 AN: 5182

South Asian (SAS) AF: 0.324 AC: 1562 AN: 4824

European-Finnish (FIN) AF: 0.323 AC: 3418 AN: 10578

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29632 AN: 67938

Other (OTH) AF: 0.368 AC: 778 AN: 2112

Alfa AF: 0.387 Hom.: 32158

Bravo AF: 0.309

Asia WGS AF: 0.258 AC: 895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.6
DANN	Benign	0.78
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs11205277; hg19: chr1-149892872;