rs1744659

Variant names:

• chr6-36548590-T-C
• rs1744659

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.493 AC: 20396 AN: 41380

American (AMR) AF: 0.348 AC: 5304 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 425 AN: 3472

East Asian (EAS) AF: 0.163 AC: 840 AN: 5152

South Asian (SAS) AF: 0.160 AC: 770 AN: 4816

European-Finnish (FIN) AF: 0.157 AC: 1655 AN: 10548

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8572 AN: 67968

Other (OTH) AF: 0.234 AC: 494 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.24

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1744659; hg19: chr6-36516367;