rs1001455

Variant names:

• chr4-162338467-G-T
• rs1001455

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 0.0292 in 152,178 control chromosomes in the GnomAD database, including 141 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 0.029 (141 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0817 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: 0.0292 AC: 4436 AN: 152060 Hom.: 141 Cov.: 31

Gnomad AFR AF: 0.0472

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0776

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.0882

Gnomad SAS AF: 0.00870

Gnomad FIN AF: 0.00774

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00904

Gnomad OTH AF: 0.0239

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

GnomAD4 genome AF: 0.0292 AC: 4439 AN: 152178 Hom.: 141 Cov.: 31 AF XY: 0.0298 AC XY: 2219 AN XY: 74394

Gnomad4 AFR AF: 0.0471

Gnomad4 AMR AF: 0.0776

Gnomad4 ASJ AF: 0.0150

Gnomad4 EAS AF: 0.0884

Gnomad4 SAS AF: 0.00871

Gnomad4 FIN AF: 0.00774

Gnomad4 NFE AF: 0.00904

Gnomad4 OTH AF: 0.0237

Alfa AF: 0.0234 Hom.: 27

Bravo AF: 0.0368

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.5
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1001455; hg19: chr4-163259619;