rs1145724

Positions:

• chr6-90477791-T-C

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 0.26 in 152,144 control chromosomes in the GnomAD database, including 8,370 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 0.26 (8370 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

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 (AFR) allele frequency at 95% confidence interval = 0.578 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: 0.260 AC: 39587 AN: 152026 Hom.: 8361 Cov.: 33

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.0815

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.260 AC: 39630 AN: 152144 Hom.: 8370 Cov.: 33 AF XY: 0.257 AC XY: 19120 AN XY: 74424

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.0112

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.246

Alfa AF: 0.154 Hom.: 4806

Bravo AF: 0.272

Asia WGS AF: 0.134 AC: 467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1145724; hg19: chr6-91187510;