chr1-154391664-G-A

Variant names:

• chr1-154391664-G-A
• rs11265608

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 0.1 in 152,194 control chromosomes in the GnomAD database, including 816 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 0.10 (816 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.603

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 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: 0.0999 AC: 15191 AN: 152076 Hom.: 811 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0602

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0367

Gnomad SAS AF: 0.0433

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0995

Gnomad OTH AF: 0.0834

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

GnomAD4 genome AF: 0.100 AC: 15221 AN: 152194 Hom.: 816 Cov.: 32 AF XY: 0.101 AC XY: 7504 AN XY: 74384

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0601

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0368

Gnomad4 SAS AF: 0.0429

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.0995

Gnomad4 OTH AF: 0.0859

Alfa AF: 0.0960 Hom.: 369

Bravo AF: 0.0938

Asia WGS AF: 0.0660 AC: 231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11265608; hg19: chr1-154364140;