chr1-149920979-A-G

Variant names:

• chr1-149920979-A-G
• rs11205277

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.368

Alfa AF: 0.402 Hom.: 19958

Bravo AF: 0.309

Asia WGS AF: 0.258 AC: 895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11205277; hg19: chr1-149892872;