chr1-153461378-A-T

Position:

• chr1-153461378-A-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The variant allele was found at a frequency of 0.00177 in 152,094 control chromosomes in the GnomAD database, including 3 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 0.0018 (3 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.13).
• BS2: High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00175 AC: 266 AN: 151976 Hom.: 3 Cov.: 33

Gnomad AFR AF: 0.00189

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00413

Gnomad ASJ AF: 0.00374

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.00394

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000985

Gnomad OTH AF: 0.00144

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

GnomAD4 genome AF: 0.00177 AC: 269 AN: 152094 Hom.: 3 Cov.: 33 AF XY: 0.00203 AC XY: 151 AN XY: 74376

Gnomad4 AFR AF: 0.00196

Gnomad4 AMR AF: 0.00412

Gnomad4 ASJ AF: 0.00374

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.00394

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.000985

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.000583 Hom.: 0

Bravo AF: 0.00169

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.13
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3124216; hg19: chr1-153433854;