rs1744659

Positions:

• chr6-36548590-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 0.254 in 151,912 control chromosomes in the GnomAD database, including 6,947 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 0.25 (6947 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 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: 0.254 AC: 38556 AN: 151794 Hom.: 6907 Cov.: 31

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.254 AC: 38648 AN: 151912 Hom.: 6947 Cov.: 31 AF XY: 0.254 AC XY: 18853 AN XY: 74260

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.234

Alfa AF: 0.205 Hom.: 601

Bravo AF: 0.285

Asia WGS AF: 0.193 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1744659; hg19: chr6-36516367;