rs1555089

Positions:

• chr6-24648178-G-A
• chr6-24648178-G-C
• chr6-24648178-G-T

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 0.703 in 152,100 control chromosomes in the GnomAD database, including 38,181 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 0.70 (38181 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

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: 0.703 AC: 106894 AN: 151982 Hom.: 38153 Cov.: 32

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.703 AC: 106973 AN: 152100 Hom.: 38181 Cov.: 32 AF XY: 0.700 AC XY: 52025 AN XY: 74330

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.875

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.712

Alfa AF: 0.659 Hom.: 6522

Bravo AF: 0.725

Asia WGS AF: 0.793 AC: 2756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.057
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555089; hg19: chr6-24648406;