chr1-154580974-T-A

Position:

• chr1-154580974-T-A

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 0.627 in 152,144 control chromosomes in the GnomAD database, including 31,004 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 0.63 (31004 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95346 AN: 152026 Hom.: 30991 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.627 AC: 95389 AN: 152144 Hom.: 31004 Cov.: 32 AF XY: 0.632 AC XY: 46982 AN XY: 74390

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.766

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.639

Alfa AF: 0.565 Hom.: 1795

Bravo AF: 0.624

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.2
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6656743; hg19: chr1-154553450;